Septra is pretty old-school--it's a sulfa drug so it's one of the first types of antibiotics discovered. Baytril might still work, but since she's had LRI before, and it was more than a year ago, I would still suspect that Baytril is probably not the best choice. It is fairly expensive to do the diagnostic to tell if it's being treated since it's otherwise asymptomatic (x-ray), so going with the "big guns" in a bunny at middle age is probably a good idea. With younger buns you worry about breaking out the newer, stronger antibiotics because they have many many years left, and if you get their resident bacteria resistant to the top-of-the-line antibiotics at a young age, you can run out of antibiotics to use by the time they get old. In a middle-aged bun, that's not as big a concern. It might be time to break out the Zithromax (although it can cause more GI issues than Baytril), Pen G, chloramphenicol, or Convenia. Convenia is probably the most convenient one because the vet injects it once every 5 days.
Another thing you might want to try is nebulizing. It can take a while to find one, so I'd start looking now. You can usually get a nebulizer for less than $60 off craigslist or ebay. Sterile saline water or solutions you'd use for human nasal irrigation (think Neti Pot) can be used as the solution, or the doctor can have you nebulize antibiotics as well. Saline nebulization really helped our Benjamin with pneumonia. They tolerate it ok as long as it's only once a day for less than half an hour, and I think doing a nebulization chamber is better than the mask.
