KITLIST.2DA is specific to each user's install, depending on what kits they have installed in what order. So you may have unknowingly wiped or overwritten it or something.
I find it is best to assign kits to CREs on install via tp2 or ingame, as this ensures the correct kit is added to the creature.
If you create a creature of a new kit and save and export that .CRE, for example, then the value that CRE's kit has in KITLIST.2DA may well be different from the value the kit has on someone else's install, causing the creature to not have the right kit for them, with the resulting loss in abllities and so on.
So... You need to install the kit first in your tp2, then any assignments you make or scripts you compile will be correct for the end user. If that's what your asking.