Non-recognition aggression, HELP

Hey cat lovers, I need advice.

I have two cats who are litter mates and have been together their whole lives. They are best friends and have a very sweet relationship.

Banjo (male) went to the vet Friday night for insecticide ingestion and was there until Saturday afternoon. He wasn't doped up or anything at the vet, he was just given fluids and monitored. He is currently taking antibiotics though to help his intestines.

When I brought him home, I immediately took him out of his carrier expecting Harper (female) to welcome him home with purrs and licks and snuggles. Instead she's been hissing and growling at him.

I gave him a bath and rubbed him down with things that smell like Harper in hopes that would make him smell normal. But it's been two days now, and she's still hissing at him and avoiding him. They've gotten a tiny bit better and will be in the same area as long as Aaron or I am there too. We've also tried calming, pheromone spray, but haven't seen much improvement from that.

It's breaking my heart. Has anyone encountered this before, and what d'you suggest doing? Harper hasn't tried to hurt him, and I doubt she ever would. She just hisses and runs away from him, or he'll run away from her. I've read we should try separating them, but we have a tiny, one-bedroom apartment and only one litter box, so that's not really an option.

Help, please!

Sometimes it happens. The best thing that comes to mind is an episode of Cat's from Hell. Separate both cats either with a door, or kid fence so neither cat can attack each other. During feeding time, feed them near each other with the door closed. The idea is to associate something good with each other's sent. After a few days, gradually remove the door (fence, towel, whatever is separating them). If one starts to hiss or growl, then they aren't ready yet. Over a week or so you should be able to re-introduce them. 

http://www.animalplanet.com/tv-shows/my-cat-from-hell/videos/ Harold and Ninja is a quick example.

What you are experiencing is quite common. Banjo got sick, spent some time at the vet, and is now on medication. His exposure to scents away from home made him a "different" cat to Harper. 

Your way of acclimating Banjo is correct. Harper does not seem that aggressive so wait a few more days. She will probably be suspicious while Banjo is on antibiotics. Some cats do not like being near an ill one and tend to be more aggressive than usual. Just be around when they are together. Their relationship will go back to normal in time.