My mod has the goal to allow to enslave almost anything thats human or ghoul (no children). I don't use any leftovers from FO3 and have my own system. Don't worry I built in a lot of safeguards and if quests or mods need their NPCs they always win against mine.
That's how I detected that yours are only enslaveable for a short time because of this clever cleanup script. But it would be counterproductive for my mod if the player isn't allowed to enslave your increased spawns. MMM was pretty friendly in FO3 and made almost no troubles (a new MMM update produced a few unwanted extra spawns at a slave location, but this was actually a pretty funny effect like friends come to help ).
I made a little compatibility esp to solve this problem. I check in IWSNullSCRIPT if the NPC is in my slave faction and if yes they aren't disabled and deleted. My question was if there are other places that I should look for to avoid other 'accidents' and if this method is ok without producing troubles for your mod.
Btw. if a slave dies or is set free in my mod he/she is brought back to it's capture location and there are absolut no leftovers from my mod or any changes at the NPC. The spawn is absolutly the same NPC as it was before.