If you have photos of your cage set up and current set up, maybe that would help since I'm trying to understand what's going on.
Typically there are two common recommendations for bonding. One is to allow the rabbits together frequently for short periods of time. This would be at least twice per day for as short as 5-10 minutes each session, depending on how they are reacting. This length of time would increase as they are able and are doing well. This method starts in a confined area like a bathroom or even the tub (if it isn't overly slick). The area size would remain the same until they are showing that they are getting along without any issues for long periods of time.
The second method involves putting the rabbits together in a limited space (can be slightly larger than a typical bathroom) that has numerous boxes and diversions in the area. With this method, the rabbits are monitored continually and remain together 24/7 until they either bond or it is determined that they won't bond. Once they begin to get along without any issues whatsoever, then they remain in that same area for a week or two (longer if it has taken them long to get to that point).
With either method, once they seem to be bonded, that bond will be tested once they are moved to a different location or if their area is enlarged.
It sounds like you've been doing different combinations of various methods which may be rather confusing to the rabbits. I imagine they are not sure about what is shared territory and what is their individual territory. Normally, bonding attempts in a large area (ie. living room) can cause each of the rabbits to establish portions of the area as theirs. This is not desirable for bonding. This is why smaller areas are recommended for bonding.
Also, to be considered, is what part of the home will eventually be their exercise area once they are bonded and are sharing a cage.
All this background is given to establish some basics. Ideally, with bonding, if short sessions are being done, it really should be done in a very limited neutral space. When they are not in a session, they should each be in a separate cage. Once they are making good progress (longer sessions and more frequent sessions) there will be a time to place them together into what will be their new, shared cage. That cage should also be made as neutral as possible. If it is a new cage, all the better. If it is a cage that belonged to one of them, then it should be re-arranged, wiped down with vinegar, and items from both rabbits' cages should be placed in there. The idea is to make it seem as neutral as possible.
Once they are able to share this cage together, they should remain in there for a couple days. After that, an exercise pen (or similar) can be used to create a limited area around the new cage. They can come out and explore in this limited area only, at first. If given too much space too soon, that can cause territory issues and disrupt the bond. So limited area at first.
In time, the area can be expanded. Again, the idea here is to maintain that bond by not testing it too much all at once. Each time the area is expanded, they should be monitored. If they seem to revert, then the area is shrunken back again.
It seems, if I'm understanding your description, that they are having both good and bad moments when in the larger area of the living room and also that they may be establishing (or trying to establish) individual territories in that area. My thought would be to not continue in that area. If this will be their future exercise area, this would be even more important (that they not establish separate areas within that area). If this is your only area to use now, then using an x-pen to severely limit the space may be a better option. This forces them into the smaller space discussed already - until they are getting along without any issues.
Whew. I know that is a lot of writing. Hopefully not too overwhelming and hopefully it makes sense. Let me know if clarification is needed.
