Remember that we are not vets here - we can only give you information based on our own experiences - but I personally would not continue the Baytril without a diagnosis that required it. As I stated above, if I was going to try something, I would have gone with a bit gentler antibiotics like trimethoprim sulfa.
I would still want to find a chinchilla experienced vet to see him. A seizure "generally" only lasts as long as it lasts, then there is a bit of a down time after, they most chins perk back up to their normal behavior. Granted, Baytril is nastiness personified, and maybe that's the reason he's still not back to his usual self, but if you stop the Baytril and he doesn't perk back up he needs to see the vet.
Right now I would be sure to monitor his weight, his poop, his urine, his water intake, his food intake, and his behavior. Keep a log. I would also get the CC and the Lifeline and offer that to him to get his gut back on track.