I am having a similar problem right now. I have 2 cats as well, Bubba is 12 and Kit Kat is 2. They have lived together since Kit was a lil kitten and now Bubba went to the vet on Friday and didn't come home until Sunday b/c he had surgery. Since he's been home, it's like Kit's possessed! She's scared and hisses and growls at him and she was acting that way toward me for the first day also, but has gotten better with me. It's very strange, but I can't have her acting like this, there's no reason for it. I've been punishing her for acting that way, when I see her growl or hiss at Bubba, I've got a spray bottle of water handy and I give her a squirt in the face when she gets an attitude. Someone suggested that I take a towel and rub it on Bubba and then on Kit, to help reintroduce the scent to her and maybe make her a little bit more comfortable. I don't know what else to do. Normally, they eat, drink, sleep and play together, now she won't even stay in the same room if he's around. I don't have any more advise for you and I'm sorry for that, but I'm going through something similar in my house and I understand the frustration. I was thinking of the same idea you had, about seperating the cats, but I don't wanna punish Bubba, he's recovering from surgery and I want to just let him do what he pleases.

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