I too am in this position.
My bunnies have never been snuggle bunnies as such, but do have their moments and have generally got on okay. However, about a month ago Rosie had 2 dreadful wounds - one on the inside of one leg and the other on the outside of the other leg. She had to have surgery to repair them.
My first problem has been - I don't know how they ocurred for sure. I have 3 possibilities - the two rabbits were fighting (not typical fight wounds according to the vet, but still possible), she has injured herself in the garden or may be a cat.
Whichever reason, they have had to be separated (Rosie, spayed female and Teddy a neutered male). We are now having to do a full rebond.
Spent all day Saturday monitoring both bunnies in the bath. Very, very tiring. Their encounters were frighteningly vicious - but oven gloves to the ready, I managed to separate every bout, until the evening, when they seemed fairly settled. I slept downstairs (downstair bathroom) and had an uneventful night with them both.
Sunday, we put them both back into their original accommodation - horrendous. They were lunging at each other, very violently. It was draining and so unrewarding as no progress was made over the day. Consequently they were separated again - original accommodation but with a divider of mesh.
They will be there for the week, when we will try again this weekend. I hate seeing them like this as their quality of life is definately poorer. The accommodation is superb for 2 rabbits, but just about adequate when divided into two. They are also missing out on the free range of the garden.
Today I returned to find Teddy had jumped over the divider into Rosie's accommodation. There was evidence of fighting (fur), but I was amazed no real injuries. I don't know how long they had been together, but it has given me a tiny bit of hope. They are now again separated by mesh, with extra security measures!
I do not know how I can give 2 rabbits the quality of life they had when bonded if they have to live separately so I am sooo hoping this can be sorted.
I have had rabbits for many years and have never had such a problem before. It has been an eye opener and quite honestly, rocked my confidence.