Ah ok that makes sense then. You aren't using the new test version if there are ship overrides in the replace section of mod_info. There should only be skin files, economy files, faction files and variants in the newest (and most compatible) version.
Keep in mind that the test update (under the main download) will require you to remove or delete the old mod directory or it will cause problems.
Even with the new version, however, there are a couple of exceptions (notably the (XIV) Legion) that are still overridden with changes. Can't get around that unfortunately. Still, the vast majority of mods should be compatible with the test version and the other skin files are only overridden to remove their blueprint tags iirc.
Spoiler
"id":"archeus",
"name":"Archean Order",
"version":"1.3.5",
"author":"Morrokain",
"description":"A complete rebalance of Starsector that focuses on smaller weapons, more fighters and a heavy addition of lore content. Almost all weapons and ships have been reworked to some degree and many added. Tutorials, tooltips, descriptions and hints have been updated to explain new facets of gameplay, or, use the Tactics Manual (.doc in mod folder) as a reference! Enjoy!",
"gameVersion":"0.9.1a",
"modPlugin":"data.scripts.ArcheusModPlugin",
"jars": ["Archean Order TC v0.9.1a.jar"],
"totalConversion":"true",
"replace":[
"data\\campaign\\econ\\aztlan.json",
"data\\campaign\\econ\\arcadia.json",
"data\\campaign\\econ\\askonia.json",
"data\\campaign\\econ\\eos.json",
"data\\campaign\\econ\\isirah.json",
"data\\campaign\\econ\\canaan.json",
"data\\campaign\\econ\\algebbar.json",
"data\\campaign\\econ\\kumarikandam.json",
"data\\campaign\\econ\\magec.json",
"data\\campaign\\econ\\naraka.json",
"data\\campaign\\econ\\valhalla.json",
"data\\campaign\\econ\\samarra.json",
"data\\campaign\\econ\\mayasura.json",
"data\\campaign\\econ\\thule.json",
"data\\campaign\\econ\\tyle.json",
"data\\campaign\\econ\\yma.json",
"data\\campaign\\econ\\zagan.json",
"data\\campaign\\econ\\corvus.json",
"data/characters/skills/helmsmanship.skill",
"data\\world\\factions\\pirates.faction",
"data\\world\\factions\\neutral.faction",
"data\\world\\factions\\hegemony.faction",
"data\\world\\factions\\independent.faction",
"data\\world\\factions\\player.faction",
"data\\world\\factions\\sindrian_diktat.faction",
"data\\world\\factions\\knights_of_ludd.faction",
"data\\world\\factions\\luddic_church.faction",
"data\\world\\factions\\luddic_path.faction",
"data\\world\\factions\\persean_league.faction",
"data\\world\\factions\\tritachyon.faction",
"data\\world\\factions\\remnants.faction",
"data\\world\\factions\\scavengers.faction",
"data\\world\\factions\\lions_guard.faction",
"data\\world\\factions\\derelict.faction",
"data\\world\\factions\\poor.faction",
"data\\world\\factions\\sleeper.faction",
# Required to to avoid this spawning through Misc Theme generator.
"data\\hulls\\skins\\legion_xiv.skin",
# Required to remove blueprint tags from the TC version but otherwise untouched.
"data\\hulls\\skins\\brawler_pather.skin",
"data\\hulls\\skins\\brawler_tritachyon.skin",
"data\\hulls\\skins\\buffalo_hegemony.skin",
"data\\hulls\\skins\\buffalo_luddic_church.skin",
"data\\hulls\\skins\\buffalo_pirates.skin",
"data\\hulls\\skins\\buffalo_tritachyon.skin",
"data\\hulls\\skins\\cerberus_d_pirates.skin",
"data\\hulls\\skins\\cerberus_luddic_path",
"data\\hulls\\skins\\dominator_xiv.skin",
"data\\hulls\\skins\\eagle_xiv.skin",
"data\\hulls\\skins\\enforcer_d_pirates.skin",
"data\\hulls\\skins\\enforcer_xiv.skin",
"data\\hulls\\skins\\falcon_p.skin",
"data\\hulls\\skins\\falcon_xiv.skin",
"data\\hulls\\skins\\hound_d_pirates.skin",
"data\\hulls\\skins\\hound_hegemony.skin",
"data\\hulls\\skins\\hound_luddic_church.skin",
"data\\hulls\\skins\\hound_luddic_path.skin",
"data\\hulls\\skins\\kite_hegemony.skin",
"data\\hulls\\skins\\kite_luddic_path.skin",
"data\\hulls\\skins\\kite_pirates.skin",
"data\\hulls\\skins\\lasher_pather.skin",
"data\\hulls\\skins\\lasher_luddic_church.skin",
"data\\hulls\\skins\\mudskipper2.skin",
"data\\hulls\\skins\\mule_d_pirates.skin",
"data\\hulls\\skins\\onslaught_xiv.skin",
"data\\hulls\\skins\\afflictor_d_pirates.skin",
"data\\hulls\\skins\\shade_d_pirates.skin",
"data\\hulls\\skins\\wolf_d_pirates.skin",
"data\\hulls\\skins\\wolf_hegemony.skin",
"data\\variants\\aurora\\aurora_Assault.variant",
"data\\variants\\aurora\\aurora_Assault_Support.variant",
"data\\variants\\aurora\\aurora_Balanced.variant",
"data\\variants\\aurora\\aurora_Escort.variant",
"data\\variants\\aurora\\aurora_FS.variant",
"data\\variants\\aurora\\aurora_Strike.variant",
"data\\variants\\brawler\\brawler_pather_Raider.variant",
"data\\variants\\brawler\\brawler_tritachyon_Standard.variant",
"data\\variants\\buffalo\\buffalo_d_Standard.variant",
"data\\variants\\buffalo\\buffalo_hegemony_Standard.variant",
"data\\variants\\buffalo\\buffalo_luddic_church_Standard.variant",
"data\\variants\\buffalo\\buffalo_pirates_Standard.variant",
"data\\variants\\buffalo\\buffalo_Standard.variant",
"data\\variants\\buffalo\\buffalo_tritachyon_Standard.variant",
"data\\variants\\centurion\\centurion_Assault.variant",
"data\\variants\\centurion\\centurion_Starting.variant",
"data\\variants\\cerberus\\cerberus_d_pirates_Shielded.variant",
"data\\variants\\cerberus\\cerberus_d_pirates_Standard.variant",
"data\\variants\\cerberus\\cerberus_d_Standard.variant",
"data\\variants\\cerberus\\cerberus_Hardened.variant",
"data\\variants\\cerberus\\cerberus_luddic_path_Attack.variant",
"data\\variants\\cerberus\\cerberus_Overdriven.variant",
"data\\variants\\cerberus\\cerberus_Shielded.variant",
"data\\variants\\cerberus\\cerberus_Standard.variant",
"data\\variants\\cerberus\\cerberus_Starting.variant",
"data\\variants\\conquest\\conquest_Elite.variant",
"data\\variants\\conquest\\conquest_Standard.variant",
"data\\variants\\derelict\\derelict_mothership_bow_module_Standard.variant",
"data\\variants\\derelict\\derelict_mothership_pod_engine_left_Standard.variant",
"data\\variants\\derelict\\derelict_mothership_pod_m_left_Standard.variant",
"data\\variants\\derelict\\derelict_mothership_pod_m_right_Standard.variant",
"data\\variants\\derelict\\derelict_mothership_pod_s_right_Standard.variant",
"data\\variants\\derelict\\derelict_mothership_sensor_mast_Standard.variant",
"data\\variants\\derelict\\guardian_Standard.variant",
"data\\variants\\derelict\\rampart_Standard.variant",
"data\\variants\\dominator\\dominator_AntiCV.variant",
"data\\variants\\dominator\\dominator_Assault.variant",
"data\\variants\\dominator\\dominator_d_Assault.variant",
"data\\variants\\dominator\\dominator_Fighter_Support.variant",
"data\\variants\\dominator\\dominator_Outdated.variant",
"data\\variants\\dominator\\dominator_Support.variant",
"data\\variants\\dominator\\dominator_XIV_Elite.variant",
"data\\variants\\drones\\drone_borer.variant",
"data\\variants\\drones\\drone_pd.variant",
"data\\variants\\drones\\drone_pd_midline.variant",
"data\\variants\\drones\\drone_terminator.variant",
"data\\variants\\eagle\\eagle_Assault.variant",
"data\\variants\\eagle\\eagle_Balanced.variant",
"data\\variants\\eagle\\eagle_d_Assault.variant",
"data\\variants\\eagle\\eagle_xiv_Elite.variant",
"data\\variants\\enforcer\\enforcer_Assault.variant",
"data\\variants\\enforcer\\enforcer_Balanced.variant",
"data\\variants\\enforcer\\enforcer_CS.variant",
"data\\variants\\enforcer\\enforcer_d_pirates_Strike.variant",
"data\\variants\\enforcer\\enforcer_d_Strike.variant",
"data\\variants\\enforcer\\enforcer_Elite.variant",
"data\\variants\\enforcer\\enforcer_Escort.variant",
"data\\variants\\enforcer\\enforcer_Fighter_Support.variant",
"data\\variants\\enforcer\\enforcer_Outdated.variant",
"data\\variants\\enforcer\\enforcer_Overdriven.variant",
"data\\variants\\enforcer\\enforcer_XIV_Elite.variant",
"data\\variants\\falcon\\falcon_Attack.variant",
"data\\variants\\falcon\\falcon_CS.variant",
"data\\variants\\falcon\\falcon_d_CS.variant",
"data\\variants\\falcon\\falcon_p_Strike.variant",
"data\\variants\\falcon\\falcon_xiv_Elite.variant",
"data\\variants\\falcon\\falcon_xiv_Escort.variant",
"data\\variants\\fighters\\broadsword_Fighter.variant",
"data\\variants\\fighters\\claw_Fighter.variant",
"data\\variants\\fighters\\cobra_Bomber.variant",
"data\\variants\\fighters\\dagger_Bomber.variant",
"data\\variants\\fighters\\gladius_Fighter.variant",
"data\\variants\\fighters\\khopesh_Bomber.variant",
"data\\variants\\fighters\\longbow_Support.variant",
"data\\variants\\fighters\\mining_drone_Standard.variant",
"data\\variants\\fighters\\perdition_Bomber.variant",
"data\\variants\\fighters\\piranha_Bomber.variant",
"data\\variants\\fighters\\talon_Interceptor.variant",
"data\\variants\\fighters\\thunder_Fighter.variant",
"data\\variants\\fighters\\trident_Bomber.variant",
"data\\variants\\fighters\\warthog_Fighter.variant",
"data\\variants\\fighters\\wasp_Interceptor.variant",
"data\\variants\\fighters\\xyphos_Fighter.variant",
"data\\variants\\gryphon\\gryphon_FS.variant",
"data\\variants\\gryphon\\gryphon_Standard.variant",
"data\\variants\\hammerhead\\hammerhead_Balanced.variant",
"data\\variants\\hammerhead\\hammerhead_d_CS.variant",
"data\\variants\\hammerhead\\hammerhead_Elite.variant",
"data\\variants\\hammerhead\\hammerhead_Overdriven.variant",
"data\\variants\\hammerhead\\hammerhead_Support.variant",
"data\\variants\\hammerhead\\hammerhead_Tutorial.variant",
"data\\variants\\harbinger\\harbinger_Strike.variant",
"data\\variants\\hermes\\hermes_d_Standard.variant",
"data\\variants\\hermes\\hermes_FS.variant",
"data\\variants\\hermes\\hermes_Standard.variant",
"data\\variants\\hound\\hound_d_pirates_Shielded.variant",
"data\\variants\\hound\\hound_d_pirates_Standard.variant",
"data\\variants\\hound_d_pirates_Overdriven.variant",
"data\\variants\\hound\\hound_d_Standard.variant",
"data\\variants\\hound\\hound_hegemony_Standard.variant",
"data\\variants\\hound\\hound_luddic_church_Standard.variant",
"data\\variants\\hound\\hound_luddic_path_Attack.variant",
"data\\variants\\hound\\hound_Overdriven.variant",
"data\\variants\\hound\\hound_Standard.variant",
"data\\variants\\kite\\kite_Interceptor.variant",
"data\\variants\\kite\\kite_luddic_path_Raider.variant",
"data\\variants\\kite\\kite_luddic_path_Strike.variant",
"data\\variants\\kite\\kite_pirates_Raider.variant",
"data\\variants\\kite\\kite_Standard.variant",
"data\\variants\\kite\\kite_Starting.variant",
"data\\variants\\kite\\kite_Stock.variant",
"data\\variants\\kite\\kite_Support.variant",
"data\\variants\\lasher\\lasher_Assault.variant",
"data\\variants\\lasher\\lasher_CS.variant",
"data\\variants\\lasher\\lasher_d_CS.variant",
"data\\variants\\lasher\\lasher_luddic_church_Standard.variant",
"data\\variants\\lasher\\lasher_luddic_path_Raider.variant",
"data\\variants\\lasher\\lasher_Overdriven.variant",
"data\\variants\\lasher\\lasher_PD.variant",
"data\\variants\\lasher\\lasher_Standard.variant",
"data\\variants\\lasher\\lasher_Starting.variant",
"data\\variants\\lasher\\lasher_Strike.variant",
"data\\variants\\legion\\legion_Assault.variant",
"data\\variants\\legion\\legion_Escort.variant",
"data\\variants\\legion\\legion_FS.variant",
"data\\variants\\legion\\legion_Strike.variant",
"data\\variants\\legion\\legion_xiv_Elite.variant",
"data\\variants\\mercury\\mercury_Attack.variant",
"data\\variants\\mercury\\mercury_d_Standard.variant",
"data\\variants\\mercury\\mercury_FS.variant",
"data\\variants\\mercury\\mercury_PD.variant",
"data\\variants\\mercury\\mercury_Standard.variant",
"data\\variants\\mora\\mora_Assault.variant",
"data\\variants\\mora\\mora_Strike.variant",
"data\\variants\\mora\\mora_Support.variant",
"data\\variants\\mule\\mule_d_pirates_Smuggler.variant",
"data\\variants\\mule\\mule_d_pirates_Standard.variant",
"data\\variants\\mule\\mule_d_Standard.variant",
"data\\variants\\mule\\mule_Fighter_Support.variant",
"data\\variants\\mule\\mule_Standard.variant",
"data\\variants\\mule\\mule_Starting.variant",
"data\\variants\\onslaught\\onslaught_Elite.variant",
"data\\variants\\onslaught\\onslaught_Standard.variant",
"data\\variants\\onslaught\\onslaught_Outdated.variant",
"data\\variants\\onslaught\\onslaught_xiv_Elite.variant",
"data\\variants\\paragon\\paragon_Elite.variant",
"data\\variants\\paragon\\paragon_Escort.variant",
"data\\variants\\paragon\\paragon_Raider.variant",
"data\\variants\\remnant\\brilliant_Standard.variant",
"data\\variants\\remnant\\flash_Bomber.variant",
"data\\variants\\remnant\\fulgent_Assault.variant",
"data\\variants\\remnant\\fulgent_Support.variant",
"data\\variants\\remnant\\glimmer_Assault.variant",
"data\\variants\\remnant\\glimmer_Support.variant",
"data\\variants\\remnant\\lumen_Standard.variant",
"data\\variants\\remnant\\lux_Fighter.variant",
"data\\variants\\remnant\\radiant_Standard.variant",
"data\\variants\\remnant\\radiant_Strike.variant",
"data\\variants\\remnant\\remnant_armour1_Standard.variant",
"data\\variants\\remnant\\remnant_armour2_Standard.variant",
"data\\variants\\remnant\\remnant_armour3_Standard.variant",
"data\\variants\\remnant\\remnant_hangar1_Standard.variant",
"data\\variants\\remnant\\remnant_hangar1_Strike.variant",
"data\\variants\\remnant\\remnant_shield1_Standard.variant",
"data\\variants\\remnant\\remnant_shield2_Standard.variant",
"data\\variants\\remnant\\remnant_weapon_platform1_Standard.variant",
"data\\variants\\remnant\\remnant_weapon_platform2_Standard.variant",
"data\\variants\\remnant\\remnant_weapon_platform3_Standard.variant",
"data\\variants\\remnant\\scintilla_Strike.variant",
"data\\variants\\remnant\\scintilla_Support.variant",
"data\\variants\\remnant\\spark_Interceptor.variant",
"data\\variants\\scarab\\scarab_Experimental.variant",
"data\\variants\\scarab\\scarab_Starting.variant",
"data\\variants\\stations\\gargoyle_Standard.variant",
"data\\variants\\stations\\merlon_Standard.variant",
"data\\variants\\stations\\module_armour1_Standard.variant",
"data\\variants\\stations\\module_armour2_Standard.variant",
"data\\variants\\stations\\module_armour3_Standard.variant",
"data\\variants\\stations\\module_armour4_Standard.variant",
"data\\variants\\stations\\module_armour5_Standard.variant",
"data\\variants\\stations\\module_bastion_pd1_Standard.variant",
"data\\variants\\stations\\module_bastion1_lowtech_Standard.variant",
"data\\variants\\stations\\module_blocker1_Standard.variant",
"data\\variants\\stations\\module_blocker2_Standard.variant",
"data\\variants\\stations\\module_blocker2b_Standard.variant",
"data\\variants\\stations\\module_blocker2c_Standard.variant",
"data\\variants\\stations\\module_citadel1_lowtech_Standard.variant",
"data\\variants\\stations\\module_decor_midline1_Standard.variant",
"data\\variants\\stations\\module_decor_midline2_Standard.variant",
"data\\variants\\stations\\module_hightech_armour_Standard.variant",
"data\\variants\\stations\\module_hightech_attack_minelayer_Standard.variant",
"data\\variants\\stations\\module_hightech_attack_Standard.variant",
"data\\variants\\stations\\module_hightech_citadel_Standard.variant",
"data\\variants\\stations\\module_hightech_hangar_Standard.variant",
"data\\variants\\stations\\module_hightech_shield_Standard.variant",
"data\\variants\\stations\\module_hightech_strut_Standard.variant",
"data\\variants\\stations\\module_large1_lowtech_Standard.variant",
"data\\variants\\stations\\module_large2_lowtech_Standard.variant",
"data\\variants\\stations\\module_midline_bastion_Standard1.variant",
"data\\variants\\stations\\module_midline_bastion_Standard2.variant",
"data\\variants\\stations\\module_midline_broadside_Standard.variant",
"data\\variants\\stations\\module_midline_citadel_Standard.variant",
"data\\variants\\stations\\module_midline_support_Standard.variant",
"data\\variants\\stations\\platform1_Standard.variant",
"data\\variants\\stations\\ravelin_Standard.variant",
"data\\variants\\stations\\remnant_station2_Damaged.variant",
"data\\variants\\stations\\remnant_station2_Standard.variant",
"data\\variants\\stations\\station_derelict_survey_mothership_Standard.variant",
"data\\variants\\stations\\station_small_Standard.variant",
"data\\variants\\stations\\station1_hightech_Standard.variant",
"data\\variants\\stations\\station1_midline_Standard.variant",
"data\\variants\\stations\\station1_Standard.variant",
"data\\variants\\stations\\station2_hightech_Standard.variant",
"data\\variants\\stations\\station2_midline_Standard.variant",
"data\\variants\\stations\\station2_Standard.variant",
"data\\variants\\stations\\station3_hightech_Standard.variant",
"data\\variants\\stations\\station3_midline_Standard.variant",
"data\\variants\\stations\\station3_Standard.variant",
"data\\variants\\sunder\\sunder_Assault.variant",
"data\\variants\\sunder\\sunder_CS.variant",
"data\\variants\\sunder\\sunder_d_Assault.variant",
"data\\variants\\sunder\\sunder_Overdriven.variant",
"data\\variants\\tarsus\\tarsus_d_Standard.variant",
"data\\variants\\tarsus\\tarsus_Standard.variant",
"data\\variants\\venture\\venture_Balanced.variant",
"data\\variants\\venture\\venture_Outdated.variant",
"data\\variants\\wayfarer\\wayfarer_Standard.variant",
"data\\variants\\wayfarer\\wayfarer_Starting.variant",
"data\\variants\\wolf\\wolf_Assault.variant",
"data\\variants\\wolf\\wolf_CS.variant",
"data\\variants\\wolf\\wolf_d_Attack.variant",
"data\\variants\\wolf\\wolf_d_pirates_Attack.variant",
"data\\variants\\wolf\\wolf_hegemony_Assault.variant",
"data\\variants\\wolf\\wolf_hegemony_CS.variant",
"data\\variants\\wolf\\wolf_hegemony_PD.variant",
"data\\variants\\wolf\\wolf_Overdriven.variant",
"data\\variants\\wolf\\wolf_PD.variant",
"data\\variants\\wolf\\wolf_Starting.variant",
"data\\variants\\wolf\\wolf_Strike.variant",
"data\\variants\\afflictor_d_pirates_Strike.variant",
"data\\variants\\afflictor_Strike.variant",
"data\\variants\\apogee_Balanced.variant",
"data\\variants\\apogee_Starting.variant",
"data\\variants\\astral_Attack.variant",
"data\\variants\\astral_Elite.variant",
"data\\variants\\astral_Strike.variant",
"data\\variants\\atlas_Standard.variant",
"data\\variants\\atlas2_Standard.variant",
"data\\variants\\bastillon_Standard.variant",
"data\\variants\\berserker_Assault.variant",
"data\\variants\\brawler_Assault.variant",
"data\\variants\\brawler_Elite.variant",
"data\\variants\\brawler_Starting.variant",
"data\\variants\\buffalo2_Fighter_Support.variant",
"data\\variants\\buffalo2_FS.variant",
"data\\variants\\colossus_Standard.variant",
"data\\variants\\colossus2_Pather.variant",
"data\\variants\\colossus3_Pirate.variant",
"data\\variants\\condor_Attack.variant",
"data\\variants\\condor_Strike.variant",
"data\\variants\\condor_Support.variant",
"data\\variants\\crig_Standard.variant",
"data\\variants\\defender_PD.variant",
"data\\variants\\doom_Strike.variant",
"data\\variants\\dram_Light.variant",
"data\\variants\\doom_Support.variant",
"data\\variants\\drover_Starting.variant",
"data\\variants\\drover_Strike.variant",
"data\\variants\\gemini_Standard.variant",
"data\\variants\\gremlin_d_pirates_Strike.variant",
"data\\variants\\gremlin_luddic_path_Strike.variant",
"data\\variants\\gremlin_Strike.variant",
"data\\variants\\heron_Attack.variant",
"data\\variants\\heron_Strike.variant",
"data\\variants\\hound_d_pirates_Overdriven.variant",
"data\\variants\\hyperion_Attack.variant",
"data\\variants\\hyperion_Strike.variant",
"data\\variants\\medusa_Attack.variant",
"data\\variants\\medusa_CS.variant",
"data\\variants\\medusa_PD.variant",
"data\\variants\\medusa_Starting.variant",
"data\\variants\\monitor_Escort.variant",
"data\\variants\\monitor_Starting.variant",
"data\\variants\\mudskipper_Standard.variant",
"data\\variants\\mudskipper2_CS.variant",
"data\\variants\\mudskipper2_Hellbore.variant",
"data\\variants\\nebula_Standard.variant",
"data\\variants\\odyssey_Balanced.variant",
"data\\variants\\omen_PD.variant",
"data\\variants\\ox_Standard.variant",
"data\\variants\\phaeton_Standard.variant",
"data\\variants\\picket_Assault.variant",
"data\\variants\\prometheus_Super.variant",
"data\\variants\\prometheus2_Standard.variant",
"data\\variants\\sentry_FS.variant",
"data\\variants\\shade_Assault.variant",
"data\\variants\\shade_d_pirates_Assault.variant",
"data\\variants\\shepherd_Frontier.variant",
"data\\variants\\shepherd_Starting.variant",
"data\\variants\\shrike_Attack.variant",
"data\\variants\\shrike_p_Attack.variant",
"data\\variants\\shrike_Support.variant",
"data\\variants\\starliner_Standard.variant",
"data\\variants\\tempest_Attack.variant",
"data\\variants\\tempest_Starting.variant",
"data\\variants\\valkyrie_Elite.variant",
"data\\variants\\vigilance_AP.variant",
"data\\variants\\vigilance_FS.variant",
"data\\variants\\vigilance_Standard.variant",
"data\\variants\\vigilance_Starting.variant",
"data\\variants\\vigilance_Strike.variant",
"data\\variants\\warden_Defense.variant"]
}