Yes, this can one of the issues that crop up during bonding. I usually try remove the item that is causing territorial behaviour but I suppose that is hard for you given its the cage! Does the cage have a litter box in it?  That can often be a triggering item so you could remove that while the other rabbit has cage-free time to see if the caged bun is less reactive with the free one approaches.   Im not overly confident it will make the difference but its worth a try.  Did the girls share one of these cages before the bond was challenged?

Is it possible let each rabbit out in a different area when it’s their time to be out of a cage?  If not, would you be able to put the occupied cage up on a higher place during the time when the other rabbit has the floor space?

And how do I know when the rabbits are ready to have play time together in my room again (rather than the bathtub)

This is just  a matter of trial and error really. Once you’ve seen they are getting on well in the tub, try a new space but be prepared for things to go back a step. Its best to keep the next space limited. If you have a pen, set that up and see how they do in there. If you dont have a pen, try them out on the bathroom floor before trying the bedroom.  If they are getting on well in the new space, then you can trial the bedroom floor. At that stage, I would remove the cages from the room just in case they trigger some aggression. You could then introduce items from the cage into the room and see how they react. When you see they are acting like they were before in the shared bedroom space, you can probably be able to cage them together again. If you want to try that slowly, I would bring in the cage they are to share but remove the top. See if they both hop into the base together and are non-reactive.

Just a quick note about the fight, it does sound like one rabbit was reacting to the smell of the vet clinic. To avoid something like that happening again, you can take both rabbits together for appointments so they are never separated.  If that is not manageable, the other trick it to grab a shared item they have (like a mat or blanket) and rub that over the rabbit after they come back from the vet. Hopefully that will transfer enough of a familiar scent that their bond mate wont find anything amiss.

Ditto everything Jerseygirl said, sounds like the transition from tub back to cage was just too big of a jump, so having some intermediate “semi neutral” spots in between should help.

When you are ready to move them to their final home, you should clean the cage and litter box with a white vinegar solution to try to make it smell more neutral and reorganize the cage is possible.

Did I make a mistake with how long the bonding session was? Should I have let Freddie hump Coal? I’m not sure if this session went well or not. At this point, they don’t seem to be fighting over anything except who will be the new dominant bunny. Will that eventually work itself out, or is it possible they will keep fighting about who is the dominant one?

IMO, i dont think it was a mistake. Sure, they may not have reached that stage if the session was shorter but it’s all part of them getting to trust each other again. Sometimes they’ll get bored or want freedom from the space and act out toward the other. Ive even seen bonding rabbits together a good chunk of the day but when it’s approaching evening they start to act out. Were the fights a lot of circling, biting, fur pulling? Or batting paws, some growls, hopping away?

I do wonder how things will play out when you let them have the bedroom floor space together. The increased space and places to go hide might work in their favour. So long as they dont claim certain places or items. However, it will be more challenging for you to stop fights if they both end up having a tussle under the bed or something. When you do get to trying them in the room, if things head south, I would go back to the pen stage for more sessions before trying the room again.

It sounds like you are doing things well, the fact that they groomed after the tussling is a very good sign.

Sometimes it can take a few days of what seems like no progress and then suddenly they “click” and are fine again. So I think I would stick with what you’re doing and just keep it up. To me it sounds like you are getting there, since you’ve got grooming and playing etc, just with some disputes cropping up.

Jersey brought up a good point about boredom. I’ve noticed this too, where sometimes bunnies are just annoyed that they are stuck in the bonding area, get bored, and end up arguing. Especially at night! You might try saving some good boredom busters and/or treats for the times when they seem like they are starting to get antsy and want to tussle. Like you could save their veggies for those times, scatter their pellet ration or some treats around for them to find, give them some really nommy chew toys, etc.