This may seem… odd, but I am just wondering about how legitimate of a concern penicillin coming out actually is. For example, the rabbit itself (not even the bond mate) can simply reach back and groom the spot. When I gave my rabbit injections daily for 3 weeks, the vet never mentioned keeping an eye out about it… Without hurting your rabbit, is it possible to administer a shot and just gently press around the area to see how easy it is for penicillin to actually leak out? As previously mentioned, you can do a slight ‘massage’ to help it sink in (though the legitimacy of that, I’m unsure. It’s something we do with humans so I assume the mechanisms are the same for rabbits!).
I’m reading that they seem OK with the separate arrangement, and it’s you who is anxious for doing it– there are so many times we need to do things for our rabbits’ sakes and we feel bad about it. It’s totally possible for us to feel crappy about it and it being the safest/wisest thing to do. For example, my Wick has been confined to a small pen for over 2 months now due to a paw injury. Poor guy doesn’t understand why he lost his free-roam status, is frustrated, and I’m sad about it, and it is the best thing to do to ensure the paw heals well and is as set as possible before he’s allowed to sprint around/binky in free-roam space. All to say, if they seem OK with it and there is veterinary concern about your rabbits being together following a pencillin shot, the separation is simply temporary and will likely be tolerated well by both rabbits during this time.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.