1) Go to Starsector\mods\Arulite Starworks\data\world\factions and find the persean_league.faction file. Open the file then delete the contents and replace them with this:
Spoiler
{
"portraits":{
"standard_male":[
"graphics/portraits/arul_persean1.png",
],
"standard_female":[
"graphics/portraits/arul_persean2.png",
],
},
},
2) Save & exit this file, if you are starting a new game you shouldn't run into any issues, however, if you are mid-playthrough you will need to enable devMode and save in order to 'refresh' the known ships.
3)To do this go to Starsector\starsector-core\data\config and open settings.json, devMode should be on line 10 and you will need to change the 'false' to 'true' then load your game and save. Next exit Starsector and disable devMode following the prior instructions, this time changing 'true' to 'false'.
You should now have the Conquest and Pegasus spawn in your Persean fleets/markets again alongside the Garuda. This is an issue that will be resolved for the next update of Arulite so you will not have to manually make these adjustments in the future
probably.