Hello, I just wanted to give an update.
I took them both to the vet, and Dori was fine, but Enkei needed a little surgical procedure. He had to be put under that the vet sutured up his eyelid. He should be healed up in about 2 weeks...my poor baby
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I talked to the director of the House Rabbit Society about the whole thing. She is a pro at bonding rabbits, it's pretty much a big chunk of her job lol, so I was hoping she'd call me. We were trying to pinpoint triggers. My husband was a genious, and though of a possible trigger. In the past couple of weeks hour apartment has been really warm and humid. We have the central air fan running 24/7 (not the AC just the fan), and anytime we leave the house we always leave a tower fan oscillating in front of their cage. However, the apartment still gets muggy even with windows open. At night its pretty warm too, but we try to turn on the AC periodically when we are home. This also coincides with the recent fights. So we are wondering if that might be a trigger, crankiness from the temperature. She did obviously recommend a break for them, having the cage split and not leaving them alone in the cage for a while. But she also didn't recommend completely separating them. She feels that even though they've had these fights, the fact that they still get along well during free roaming time, and they constantly groom each other, that they can be ok, they just need some more work.
When we got home we let Enkei rest alone on his side of the cage. Later on when we let them out the first thing Enkei wanted to do was run to Dori and put his head under her chin for grooming. She started grooming his forehead and head and he was in heaven, he just wanted to be comforted by her. My husband was cracking up, he is going back to the bun that hurt him to begin with, crazy rabbits. They are still a little nervous around each other here and there so I'm keeping a close eye on them.
I'm saddended by this whole thing because we just took a few steps back in the bonding process, but I'm not losing hope. Like you all said, live and learn, and now I know to follow my gut.
Thank you all for the great advice and well wishes