Aggressive Bunny

We have 2 lop dwarf female bunnies. We purchased them September 2015 when they were still young and have never had any issues with them.
Earlier his year they starting trying to mate each other and this started to cause a few scuffles between them. We decided to have them both spayed (also for the health side).
They were both spayed almost 3 weeks ago.
After a Day or 2 pepper (the bigger bunny) started pulling fur from around the shave site out and her skin became very red. We took her to the vets and they said that they think she had an allergic reaction to the antiseptic wash they use (everyone vet at the practice said they'd never seen this before) and prescribed some steroid ointment to apply.
A couple of days later she started fighter with her sister (salt, slightly smaller bunny) so we separated them. A day later we took Pepper to the emergency vets as she became lethargic and stopped eating & drinking. They admitted her for 48 hours as the skin had become infected and she was dyhydrayed.
She has now been home for a week (tomorrow) and is much better although the fur hasn't quite grown back and Her skin is still quite scabby.
My issue is that she keeps going for her sister whenever we put them together. Salt is fine, it's always Pepper. Will this behaviour stop?
Pepper is also becoming very wary of human contact (I still have to give her oral meds twice a day & she really hates it). We try and sit with her and feed her treats but nothing works and she huddles in a corner until we've gone (even if this is for over an hour).
They are separated but can see and smell each other through some wire and we swap them over every 24 hours to try and stop them from getting territorial.

It might be she's generally grumpy as she's sore and people keeping poking her and upsetting her routine (for good reason but she doesn't know that). They'll also smell weird to each other and rabbits use scent to identify each other - it might be she smells too much like vet or meds and not like herself so they are acting as if the other is a stranger.

I would keep them separate for now, if they are aggressive through wire put something solid up. Then once they have healed and settled and are back to smelling like they should, try introducing them on neutral territory like you would rabbits that didn't know each other. Try to avoid situations in the mean time where they can scuffle as they can hold grudges.

Hi, thank you for your reply,
I was thinking along the same lines (she's still uncomfortable) but I hadn't thought about smelling different. Pepper has been through so much, the poor thing, she is the one going for the salt (who is all healed and healthy). Pepper isn't being aggressive through the wire, just when we put them together in mutual territory, sometime they sit and ignore each other, or salt will go up to pepper and say hi or the other way around. They'll smell each other's bottoms (didn't know rabbits did this, never seen it before and we've had lots of them). Pepper is fine then just suddenly goes for Salt.
Salt never fights back and just runs away to hide.
At this point we seperate them both again.
My other issue is that we are moving in a week or 2 and we need to buy new hutches, could this upset pepper further or could it be a new beginning for them and just what they need?

I would be inclined to keep your bunnies separate for now - if you allow then a couple of months for hormones to settle and also to get used to a new home, then try them together in a neutral area. I wouldn't try to rush things if I were you. Good luck with the move and hope you are able to get the girls back together eventually.

They have a blind spot right in front of their nose as their eyes are on the side of their head so when they are right up close they'll be using scent for ID.

The new home could work out a good thing, although it will be a little unsettling at first, I think neutral territory will be key so I wouldn't let them interact in the meantime. If you leave it a little as tonibun say's they'll also have lost the hormones which should help too.

Thank you both for your advice,
I really hope we can put them back together sooner rather than later.
Let's hope that the new home will be good for them.
We're back at the vets this Wednesday (hunk this'll be the 7 time in 2 months!) and I'll talk to the vet again about it.
Salt is so scared of Pepper and I think that is half the problem.
Just did a 15 minute bonding session with some lettuce (both their favourites) and they were fine apart from Pepper pushing her front paws towards Salt (what does this mean?) and Salt just hope away like a real little scary cat. Pepper can't even move when there together and Salt hides.