The official bonding process should occur when both rabbits have reached one-month-post their respective neuter/spay — note a male can still impregnate an intact doe up to 6 weeks after a neuter, so make sure the separation is definitive during the time he’s neutered and she is not yet spayed.
As you mention, baby bonds are not true bonds so there is not going to be the significant amount of distress we worry about when separating a legitimate bonded pair — you can have them see each other visually, but pens should have at least a 3in gap between so there’s no chance of fighting, in addition to pregnancy (reports of breeding through a cage wall have been reported).
Re: when to start pre-bonding, you can do it whenever (ex. swapping pens, swapping litterboxes, etc..). From my personal and moderation experience, I have a firm belief that if a bond is going to “work”, it’s not going to be contingent on when exactly you start pre-bonding or anything really that is “gained” prior to both rabbits being spayed/neutered, with exception of getting negative interactions between the two, which will hurt the chances of the bond. Therefore, your question about whether it is OK to start pre-bonding and whether any progress will be “reset” is a bit moot for me, since if the bond is meant to work, as long as you go through the proper bonding procedures when it’s time, it should: https://binkybunny.com/infocategory/bonding/ .. you can totally start pre-bonding, and if it “resets” (which arguably there’s no way for us to actually know whether or not this happens), then OK — no harm no foul!
Please note that the purpose of pre-bonding is to get the rabbits accustomed to each other’s scent, so if there is concern about them being separated and starting pre-bonding ASAP, keep in mind that pre-bonding in no way involves them interacting with each other — just each other’s stuff. Again, you can still house them side by side as long as there is a gap.
Don’t let this be a huge stressor in your life right now because at this time, with two intact rabbits, you just need to keep them separate — that’s it. You don’t need to do anything regarding bonding literally until she is one-month post-spay honestly. They will be fine separated during this time.
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.