Warning - this is long!

I have two cats who were littermates and never separated in their
three years. Until this week they've had a wonderful relationship and
we lived in peace and harmony.

Monday I took the male to the vet for a minor problem. When he
returned, he smelled from the disinfectant the vet used on his exam
table. (For future reference, I was told they suggest you put a dot of
alcohol between the shoulderblades of the cat waiting at home - where
they can't lick it - so when you bring the cat who visited the vet
home they both smell the same.) When his sister smelled him, she
became very upset and hissed and growled at him. She went under the
bed and wouldn't let him come near her. He was confused by her
rejection and upset she was growling at him. After a few minutes, he
ran after her under the bed and I had to break up a fight. She
continued to act badly towards him all evening, and I had to separate
them overnight.

In the morning he had forgotten everything and went over to greet his
sister. She was frightened because she remembered he had attacked her
and continued to hiss and growl. I had to leave for work and didn't
want them fighting while I was gone and so I separated them again.

When I was home in the evening I didn't separate them. She stayed
mostly under the bed, but came out to go on the catpole next to my
window. If her brother jumped up on the windowsill, she didn't run
away but when they were on the ground together she felt threatened by
him. He's totally confused by her behavior, but also feels threatened
and upset by her growling at him. He slinks on the ground as if he's
going to attack her again, but I can tell this is a reaction and he
really does want to be friends with her if she would only let up.

Today was the first breakthrough. I fed her in my room as usual, and
brought his food in there too. I put the bowls about 2 feet apart, and
they ate, eyeing one another suspiciously but without her growling. I
decided not to separate them as I was only going to work a half day
today, and when I got home he was sleeping under the bed and she was
on the cat pole next to the bed.

I made sure to give them each a lot of attention and affection. I
brought her into the living room - the first time she'd been there
since Monday! - and put her on my lap and made a fuss over her. He
came over and she went down to the floor. They laid down facing one
another a few feet apart, and she didn't stop growling. She got up to
walk into my room, and he got up and chased her inside. This was a
major setback.

Now I don't know what to do. Should I keep them apart and gradually
introduce them again under supervision? I'm afraid she's never going
to stop growling at him now. This is so upsetting and I feel like I'm
in a nightmare as they've always be inseparable before. Help!