I've made a mod that adds two new NPCs - a blacksmith and a general goods trader. They have their own custom factions as well as their own custom AI Packages (work, sandbox, sleep), and one has a locklist too. I tested them out carefully and was sure they functioned correctly.
I tried cleaning my mod with TES5edit - undeleting and disabling references, and removing identical to master records. After cleaning, my new merchants now no longer behave correctly, their schedule is all over the place, the shop is locked during working hours or they work through the sleep package.
So, it's quite obvious that I can't just use the built in cleaners like that. But, does any have any idea why specifically that's happening (is it removing something in particular?) and what's the best solution/work-around?