It doesn't matter how you interact with them, if you're going the genocide route you instantly kill them.How did you interact with the cats? Listened or kept threatening? Also what colour was the safe state? Because I threatened them and immediately after checked back in the store and the prices were still 999999; they went back to normal after leaving and re-entering the alley, but the save is still red. I'm missing 2 rabbit fur, however; I'm assuming I have to get them before 2.2? Or can I still get them afterwards? (I seem to remember an interaction with M.Rabbit in the cemetary about the little girl whose diary we found in the building, but I'm not sure when it was...)
The mother rabbit interaction is after reading both the notes I think, it happens automatically at the end of the chapter if you read them. Not sure about the two missing fur though.