Hi Phoebe,
The direct answer to your question is that the infection was probably never resolved to begin with. There needs to be a culture and sensitivity test performed to see what pathogen is the root cause of the infection. The sensitivity test will show what drugs will control the bacteria. It might not even be bacteria, could be something viral or even yeast....but a C&S will show that. And the bacteria could be resistant to Baytril....simply means that the bacteria has evolved and has built up an immunity to the drug. While Baytril is the drug of choice of many vets due to it's proven safety and effectiveness....the effectiveness is quickly going away as this drug has been totally overused and abused. An example in humans is penicillin. At one time, it was hailed as a miracle drug....now it's virtually useless due to the same issues. While I do still use Baytril sometimes, I very rarely use it as a first line treatment. It is nearly always used in support of another drug or as a "mop up" treatment. I live near a vet school and there are actually quite a few rabbit savvy vets (including several teaching professors) and most of them do not use Baytril in rabbits any longer. I am personally hoping that more vets will attend these conferences in which new treatments are presented. That will be the quickest way to get these new treatment protocols out there in the hands of the doctors.
Treating ear infections can take several different medications, require additional husbandry support and may take a long time to resolve. I have treated ear infections for as long as 8 months. We have been successful in correcting every tilt case that originated in our rescue. We have one lionhead with a very slight tilt...came from an untreated case of mites with secondary bacterial infection....and we corrected about 90%. He was tilted all the way over upon admission to our rescue. We have another, a Hotot with blue eyes, that is totally twisted and most likely will never correct. He came from a pet store chain.....they did take him to a vet but he was misdiagnosed as having a "brain worm"(E Cuniculi). Unfortunately for Sparky, that misdiagnosis meant the actual ear infection was left untreated and the damage to the ear is done. He will never correct but we do have husbandry protocols in place for him and he lives as a very happy rabbit....he runs and plays....but he literally has a very twisted view of the world.
Bottom line....get a culture and treat aggressively based on the findings of the C&S. Time is against your rabbits as the longer the infection is active in that ear, the more damage is done that might not be repairable.
Randy