I’m sorry you’re going through this, it sounds stressful!
I’m sorry to ask, but are you 100% sure she is spayed? It sounds like the behaviour of an unspayed female. We had someone just the other day adopt a boy who they thought was neutered, but it turned out he wasn’t. In a way, if she isn’t spayed that’s quite an easy fix.
If she definitely is spayed, then it’s trickier to know what to do. Some rabbits really just won’t bond with other rabbits, but it’s odd that they got on, then she got aggressive. It could be that she’s one of those. It could be that you bonded them early before she was fully settled, and then once she felt more settled in her home she became more aggressive. How long have you had her now? How much space does she have in her pen?
If you want to keep Indie in your room, perhaps you could try keeping a shower curtain over your bedspread, which would discourage him from peeing on it, and make clean up easier if he did.