Technically, you are not “rebonding” them because a baby bond is not considered a “real” bond. You are correct that there are many rabbit owners with male-male pairs, and these are stable and secure bonds as they are between two neutered males (not young and hormonal ones). Those you see who are young/intact are likely to dissolve, similar to what you’ve experienced.
Yes– after they are neutered and you wait a month to allow the hormones to dissipate, you need to go through the actual rabbit bonding process. If they are not compatible, then yes, they need to remain separate indefinitely. Judgments on whether or not they are compatible can’t be discerned right now, so just focus on keeping them separated and getting them neutered. Whether or not they bond will only be negatively impacted if you allow interactions between them and therefore accumulate a history of negative, unpleasant interactions (what has happened so far won’t do anything permanent to their chances of bonding later. Just don’t let them interact again until actual bonding).
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.