I adopted two male neutered rabbits almost two years ago.  They were bonded before I adopted them.  Recently, the dwarf, Stuart, was in the hospital for a couple of days due to GI stasis.  He came home a couple of days ago.  I was keeping the two separate so I could gauge how much Stuart was eating.  He was super unhappy in the small puppy playpen I had him in and was not eating.  Thinking maybe he needed his buddy (he was always super dependent on Bob), I set sectioned off part of the large pen they live in just for him so Bob could not eat his food but so they could see each other and boop snoots.  Stuart’s appetite improved, but not by much.  I decided (unfortunately) to let them out together this afternoon so they could be together, as the separation seemed to be stressing out Bob (and I didn’t want him going off his food either).  All day Bob had been hanging out right on the other side of the bars from Stuart, no problems.  I let them out together and kept my eye on them.  They seemed fine, Stuart was grooming Bob like he always does.  A minute or two after I turn my back, I hear a huge ruckus.  I run in there to find Bob chasing Stuart and fur flying, large chunks of it, all from Stuart.

I separate them by putting them back in their respective pens, but Bob is on high alert now and keeps following Stuart around the outside of his pen, like he is stalking him.  His tail is up the entire time.  I did some reading and saw something about switching who is in which pen when trying to bond, so I decided to try that.  I also thought it might help Stuart if he has a little more room to roam.

Well, Bob manages to bust out of the little pen and attacks Stuart again.  I break them up by grabbing Bob, who is now in “time-out” in the small puppy pen Stuart was in previously.  Bob is not happy about it, but I don’t have anywhere else to put him where I can trust he won’t chew on things that may be dangerous.  Stuart I gave free run of the big pen, since he is still not doing right (and this stress certainly won’t help!).  Bob will need to stay in the puppy pen for a couple of days, or at least until tomorrow afternoon when I can maybe rig up something in one of our bathrooms.

My concern now is trying to re-bond them, if it is even possible with these two.  I am worried that Stuart is now permanently afraid of Bob (he hid in a tunnel outside the pen for a while, and when he went back into the pen, he made the super-unhappy bunny squeak, which I have never heard him make before).

I am not going to try anything with the two of them for a couple of days, not until after Stuart has finished his meds (and hopefully is eating normally again).  But I am afraid that their bond may be broken for good (and that I will have to rehome a rabbit).

Has anyone else dealt with something similar or have any advice?

Thanks in advance.