I might have an issue that may involve another mod.
My playthrough (0.95a) had a persistent problem concerning fleet bloat; Vayra's Sector is included, and for some reason there's some weirdness going on concerning how Vayra's Sector deals with bounties, as the mod had additional systems concerning that aspect. In short, there would be these faction bounties that would fail to despawn when they expire, and leave behind small Neutral-affiliated loiter fleets that wander around their assigned planets indefinitely. Recently, when I checked how many of theses fleets were wandering about in my game using your mod commands (which is the 1st time I check, by the by), it had counted nearly 1200+ of these Neutral fleets flying about since the start of the game, and I have my suspicion that this was partially the reason as to why my game had trouble saving after a sufficient duration of game time.
I have used the "csmartclear" command several times before I checked the fleet count for the 1st time, so the command clearly isn't fixing the problem. So I used the "cclearfleets" command to wipe clean all of the Neutral fleets, and initially it seemed to work. But when I saved my game and loaded the game after that, my campaign fleet size had completely shrunk to its smallest radius, my logistics counter no longer reacts to me shuffling my ships at the fleet screen, and the game UI fails to account of me storing my ships somewhere else, reverting to my fleet's previous state as soon as I leave the Fleet screen. The game does account for me storing my ships somehow, as soon as I save and reload the gamesave, but this obviously would be highly annoying to deal with, and reloading the game doesn't make the problem go away. Wondering if you have heard of this sort of problem before, and maybe have a suggestion on the matter.
Here is my modlist, for the know (100+ mods):
"enabledMods": [
"yunrutechmining",
"1 - VIC recombobulation",
"pantera_ANewLevel25",
"advanced_gunnery_control_dbeaa06e",
"arbuzwork",
"ARC",
"aria_compt",
"armaa",
"raccoonarms",
"automatedcommands",
"timid_admins",
"beyondthesector",
"yrutl",
"HMI_brighton",
"CWSP",
"CaptainsLog",
"capturecrew",
"Csp",
"clearCommands",
"chatter",
"timid_commissioned_hull_mods",
"COPS",
"lw_console",
"Dabble",
"istl_dassaultmikoyan",
"DetailedCombatResults",
"diableavionics",
"dialog_minimap",
"DisassembleReassemble",
"dynamictariffs",
"edshipyard",
"extra_system_reloaded",
"XLU",
"HHE",
"FPE",
"fleethistory",
"fleetsizebydp",
"GMDA",
"HMI_SV",
"HMI",
"gunnyhegexpeditionary",
"hte",
"holyludd",
"sun_hyperdrive",
"hyperionsystems",
"IndEvo",
"timid_xiv",
"kadur_remnant",
"kazeron",
"LTA",
"lw_lazylib",
"ArkLeg_Alice",
"ArkLeg",
"luddenhance",
"mag_protect",
"MagicLib",
"Mayasuran Navy",
"missingships",
"su_CarrierHullmod",
"more_hullmods",
"nexerelin",
"objects_analysis",
"OcuA",
"Ocutek",
"luddandlions",
"old_hyperion",
"ORA",
"wisp_perseanchronicles",
"Recovery_Shuttles_Buff",
"rotcesrats",
"roider",
"ryaz",
"SCY",
"Seafood",
"SEEKER",
"shadow_ships",
"swp",
"speedUp",
"sun_starship_legends",
"stelnet",
"StopGapMeasures3",
"superweapons",
"tahlan",
"Terraforming and Station Construction",
"Templars",
"perseannavy",
"TORCHSHIPS",
"transfer_all_items",
"underworld",
"US",
"ungp",
"UGH",
"vic",
"vayrasector",
"vayrashippack",
"whichmod",
"XhanEmpire",
"yrxp",
"audio_plus",
"astroidships",
"prv",
"shaderLib",
"ShipCatalogVariantEditor"