REPLACE_TEXTUALLY kicks ass.
The format is like this:
COPY_EXISTING ~kit.ids~ ~override/kit.ids~
REPLACE_TEXTUALLY ~old text~ ~new text~
That way you'll only replace the existing, broken entries, and leave any potential others alone.
The tricky thing about adding to kit.ids is that your kit might be installed in any potential order on top or below other kit mods, so to actually patch to kit.ids you'd need to do some READ_BYTE'ing to find out which number your kit has in the kitlist.2da file. As I understand it, CamDawg pr Idobek from Gibberlings three seem to have that stuff wrapped around their pinky finger, so if they come along and see this, perhaps they'll reply with some good instructions on how to do it.