By 12 weeks, young rabbits must be separated. But there are cases with very early sexual maturity, so it’s really best if you separate now. They should still be kept in the same room, but they can mate through cage bars, so you need a little bit of space between the cages or some sort of shield around the cage when one bun has play-time outside the cage and the other hasn’t. As long as they can hear and smell and see ech other, their bond will most likely not be broken by separation since they have grown up together. Once the de-sexings are done and the buns have healed (allow a month), you re-bond them. Re-bonding shouldn’t be a problem then, since they’ve never really been away from each other.
It’s important to not let the buns together too soon after their spay/neuters. The first time after a spay/neuter the bun goes through a period of hormonal imbalance that lasts a few weeks for a boy and at least a month for a girl. During that time the buns can become extra sexually aware with everything that follows – territorial aggression, pee- and poop-marking, excessive humping/courting etc. That’s not a good time to bond two buns, for obvious reasons. Wait it out, then re-bond.
All bunny-owners have been newbies at one time. We are happy to have you here =)