Fighting after hospitalization

[Senpai]

Hello and thank you for having me!
I have some issues with my bonded rabbits after one had to stay in the hospital.
So, I have three bunnies (all spayed/neutered as soon as they got old enough), Pumpkin (3 years old, female), Piwik (2 years, female, probably deaf) and Sniff (1 year, male). Until now, they all have been bonded, during day time they are free-range and during night time in their huge cage.
Last week Piwik stopped eating and she got hospitalized, diagnosed with E Coli overgrowth, got her meds and was discharged after 36 hours. I expected her to have issues with Pumpkin because she has sometimes chased Piwik and pulled hair out of her butt, but Sniff has always been super affectionate with both Pumpkin and Piwik, so I didn't expect anything bad from him, but in the end, Pumpkin has been calmer than ever and Sniff is the one chasing and pulling hair.
By now Piwik is done with her medications and they do get along in their cage (was cleaned with vinegar mix and antibacterial wipes when Piwik was feeling good enough to join back), they share a food bowl, cuddle together and sometimes Sniff even grooms her, but outside of the cage (also cleaned with vinegar mix 2x and antibacterial liquid), Sniff becomes a meanie again. With Pumpkin Piwik used to just run to the other side of the room, but she seems to be terrified of Sniff even more. As soon as Sniff even looks at her, she already is running. We did usual bonding in other rooms and they got along perfectly except Pilwik humping everyone, but this has always been like that, they got some stress bonding on top of washing machine, car rides and taking them to work with me and they always get along in other places except for their own room except humping again. Yesterday I noticed that Sniff is humping (and snorting) Pumpkin (he never humps Piwik), he does that every month for ~1-2 days and as that annoys Pumpkin, I usually just tell him to stop and he understands until he forgets and I tell him to stop again. I expect this humping to be caused by his hormonal changes as this comes an goes, so could it be that he will calm down soon and stop chasing Piwik or is there anything else I could try?
Thank you in advance!

 

[Blue eyes]

It's really important for bonded rabbits to remain together all the time. If one needs to go to the vet, it's advised to take their bondmate(s) along too. Otherwise, the bond is at risk. If only one rabbit goes to the vet, it will return smelling like a whole new rabbit.

Unfortunately, the problem appears to have compounded with a trio. It isn't just two rabbits that have to learn to get along again, but now each of the three have to sort out their standing all over again. This may take several weeks to sort out. The dynamic of their prior relationship is in flux and they seem to be testing each other's boundaries - most especially in their shared space. That free-range area is the point of contention.

The only thing I can think that could possibly help is to limit that free-range area for now. If they get along in their cage but fight in the free-range area, then you could use an ex-pen to significantly 'shrink' their roaming area outside their cage. Once they begin to be their normal selves in that smaller roaming area, gradually expand it a bit at a time. Don't expand it until they've been consistent (several days) in their getting along with each other. Gradually they should be able to work their way up to their old free-roam area.

 

[Senpai]

Thank you for ideas, I will try them out!
I am aware that they should always be together and usually, I do take them everywhere together, however, as this was a medical emergency and we rushed there midnight, they couldn't take in all three of them due to all those cables that Piwik needed and they were already overcrowded with patients. I want to believe that they really did their best and even called in their only rabbit-savvy vet at 3 am because of us, so I'm not really mad or disappointed in their decision.
And thank you once again for your input.