Non-recognition Aggression - Which Cat To Isolate?

So I brought my 8yo girl home from a 3-day stay at the animal hospital, and had no idea about non-recognition aggression. As soon as I let her out of her carrier, she let out a cheerful chirp towards the other cat, who immediately hissed at her. After a couple more hisses, I went searching on the Internet and found out the cause. I promptly put the returning cat into the guest bedroom, and after 16 hours of separation the incumbent cat still hisses when he passes the door. My question is, should I put him in isolation, since she is begging to be let out, or should I continue down this current path? All told, it could be a week like this, which I'm not exactly thrilled with.

You can swap places so that they each have some time to be less confined. Scent swapping from the rooms in this case, as well as through exchanging towels/blankets/toys for each of them should help too. Here is a TCS article that might help.

How To Deal With Non-recognition Aggression In Cats

Yes, absolutely swap them out. This will accomplish two things. No one cat will be "locked up" all the time, and both cats' scents (including that offending "vetty smell) will be all over the house. In most cases of introductions, re-introductions and dealing with non-recognition aggression, SITE swapping, not just SCENT swapping, is vital!

Thanks gang, for the responses. Right now I have them in rotating shifts in the Master Bedroom - the aggressor gets the bedroom from 8am to 8pm, and the cat brought home from the hospital gets the master bedroom from 8pm to 11pm, and then I transfer her to the guest bedroom overnight so I can sleep (she's scared of the fan I run at night). I have installed baby gates in the doorway to the master bedroom so they can see, hear, and smell each other. Bernie is still hissing as of this morning, so I imagine I have a few more days ahead of me of doing the "kitty shuffle". Both cats aren't big fans of being cooped up in the bedroom, as they're both used to free run of the house, but it is what it is right now. This afternoon is my first time being out of the house (I'm at work) with the baby gates up, so we'll see how they're acting when I return later tonight.

Let us know how it goes!

Yep, let us know! We fret, you know.