Hi,
I hope you don’t mind but I am moving this thread to the Bonding section. I would suggest you take a moment and browse through the whole section of posts on bonding. You’ll find many common tendancies among the bonded bunnies, even changes of behavior among those already bonded, and it’s chock full of useful tips and information. We also have a bonding section in the green banner above, in the drop down menu under the Bunny Info.
They’ll get along again, I’m sure, you just need to be careful to work with them slowly and be prepared to separate them if a fight breaks out.

One of my rabbits chases for fun and will occasionally pull some small tufts of fur. What you have to look for are the ears and tail – are the ears up and curious looking or pushed back against the head (that’s more aggressive). If the tail is relaxed then it’s probably nothing serious. She does this when she gets excited, such as right before she knows she’s getting fed.
You can always get a squirt bottle and spray some water at Nonny when he starts to chase

Hannah has always chased Otto a bit. For a couple months after they were bonded she chased him almost every day and would often pull tufts out of his bum. They scuffled about it a couple of times, but they’ve been fine in general. He’s learned to deal with her chasing and she’s stopped chasing so much, so they’ve worked it out. I just made sure to sleep on the couch for a bit in case the chasing turned into something more. We also had to keep them in our room at night in a small cage for a while – they couldn’t chase in the small cage.

Eddie always chased Lolli. Away from the food bowl. Out of the litter box. Completely out of the room if I was paying any attention to her. Yeah, he was a little bossy bully. I think with the food, it might be a dominance thing. Like “I’m boss of everything, don’t you forget” kind of thing. At least that’s way it seemed with Eddie and Lolli. He always chased or butted her out of the way and then started eating with her coming just a few seconds later and eating herself. After that, they’d be. I’d just watch them to make sure it doesn’t escalate into something else. But I think the dominant bunnies seem to chase from what I’ve read on the various boards here.

I have one rabbit with serious food aggression and her bonded three friends can get a good chasing. It’s part of a rabbit bond in many cases. If no injuries are suffered from this, I wouldn’t worry. Your rabbit should not stress out from this as it is a daily routine without negative consequence.

My rabbits have been bonded for several months now and my female will do the same exact thing with my male rabbit when it’s time for food.  It is like a race for me to get the food in there fast enough, otherwise, she will chase and mount him until food arrives.  I dont know if maybe she thinks he is the one giving her the food and he isn’t doing it fast enough because she does not even look to me for the food.  But once I get the food to them, all is well and they can live and eat happily together again.