You’ve provided a lot of information, so BB members who are experienced with bonding can provide some keen suggestions.
At the foundation, I believe the problem is that your rabbits are not formally bonded at all. Rabbits who are together since birth are not bonded — they get along well because they do not have territorial hormones in their system yet. It’s a very common misconception because this baby relationship can span for quite a while without showing bad signs.
After a spay, both rabbits will go through a hormonal spike as a consequence. This heavily emphasizes hormonal behaviors. So this is one thing causing the aggressive behavior.
Another thing causing it is the lack of proper bonding. Bonding is actually a formal, months long process that involves pre bonding, swapping belongings, dates, supervised hours of time, etc.. This is needed so the rabbits can really get settled with each other and override those instincts that come rooted in hormones, but can still be triggered even after a spay/neuter.
I recommend reading the bonding information provided in the BUNNY INFO section of this website.
I also encourage you to read done bonding stories and journals in the bonding section of these forums.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.