Yes, sadly, being together from birth does not create a bond. This is actually very common as they grow up and reach the aggressive teenagers stage. You need to start over bonding them as if they were strangers, but cheer up – it will probably work if you do it slowly and carefully. (See the info. section for bonding advice).
Even though you know they are both females, it would be wise to have them both neutered. It will tone down their aggression, and it will prevent both of them from getting cancer in later years, which is terrible to happen to a beloved bunny. If you can get them both done, or have the more aggressive one done first, then wait a month, you can begin bonding them. Best to have both done soon and let them heal simultaneously then start a new bonding process.
Keep them separated for now. Supervise them, have them eat and sleep separately, but keep their scents on their areas so they can continue to be used to each others’ presence in the house. I know it’s hard to have separate spaces for two that were together, but if you get something like an xpen to keep one in, you will be able to use it as an extended play area later on after their bonded. Or if one is still small, a medium sized cage can be temporary, then used later in case of emergency, or as a travel cage if you go away from home or leave them with someone else.
I know it sounds like a slow process, but it’s possible that if the vet can do the spays soon you may have two bonded bunnies again within 3-4 months if they decide to get along, and then years of happy, healthy bunnies once more.