Probiotics can be taken by humans and dogs “forever” and there is a kind for rabbits, in pellet-form, Pro-Fibre by Protexin, that can be given all the time, as a supplement. It’s not sold in the USA though but you probably have other types that are just as good. It’s from the UK and can be bought here at vet’s clinics.
You often need to take probiotics for a prolonged time for them to take effect. It’s about establishing a sound, working gut microbiota (the bacteria in our guts do LOTS of work, and in rabbits’ and dogs’ guts too), and that can be hard and/or take a long time in people and animals whose immune-systems are compromized for some reason. If Gus is on Baytril “forever” I suspect probiotics “forever” is a great idea. As you know Baytril kills bacteria, and it’s not picky, it kills the good bacteria as well as the bad ones. So if you keep replenishing the gut with good bacteria, chances are his tummy will do a lot better. People on antibiotics are recommended to take extra-high doses of probiotics. I recently did a MOOC on Gut Microbiota that was extremely interesting. It was from the University of Boulder, Colorado.
Medirabbit says you can give probiotics, they may or may not work but they won’t cause any ill effects.