It’s possible the prescribed antibiotic is working better on one than the other. Depending on their immune systems and how they’re reacting to the new environment, it could be Harley’s immune system is weaker, or the infection he has is more aggressive, or perhaps even a completely different type.
Nevertheless, it’s unusual for sneezing to go away in less than a week of treatment, so continue giving the medication. Tell your vet about how each rabbit is doing individually, and it could be that Harley needs a different medication or combination than Quinn does. I’m unsure of your vet’s experience with rabbits, but Wick had the following medications prescribed: 1) Bactrim, 2) Baytril, 3) Flocillin (penicillin). Bactrim was prescribed first, but it didn’t help so Wick was switched to Baytril. This helped a little bit, but we added on Flocillin injections and he got much better. It took about 3mo of treatment with these antibiotics to have Wick be healthy again. This is longer than the norm though because he had a very pesky infection that was extremely resilient.
Some things which could help is 1) making sure the full dose is always given, 2) whether it’s once or twice a day, make the administration regular and routine (every 12 hrs, every 24 hrs, etc..), and 3) make sure you’re alwayss using clean towels, wipes, syringes, etc.. when interacting with their noses/mouths.
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.