Did your vet ever do a culture on the saliva in the chinchilla's mouth to ensure he didn't have possibly a mouth infection of sorts(there are various strains of bacteria that cause mouth infections.)? The abscessed tooth, the other tooth being dead, all sound like familiar signs of a mouth infection. From past experience, baytril worked well with a chin I had who had a mouth infection many years ago.
The only issue is, that I was not successful in treating it quick enough, and the mouth infection got into the bone, which caused a bone infection. Unfortunately for my boy, although the baytril would get rid of the problem for the short term, once off the baytril, the mouth infection returned. It was a constant fight for about 6 months. While on baytril, he could eat fine, his teeth grew in fine, etc... once off baytril, he had dead teeth, like you mentioned, abscesses, and teeth growing out of sorts (which mimicked genetic malo.), and was needing handfed around the clock.
It was a continuous cycle, but the first way we found out it was a mouth infection was culturing the saliva in his mouth.
A mouth infection can come from something as simple as a chinchilla cutting the inside of their mouth with a water bottle tip, or poking their mouth with hay, etc... and the bacteria being on that piece of hay can lead to that.