I know this is an old thread but its a common question "how long should my herp be on X antibiotic", so I thought I would throw in my .02
Chameleons immune systems are very slow. Antibiotic treatments must be continued for a long time. I think that the number one reason that bacterial infections in chameleons don't get better is because the antibiotics are discontinued too early. Most antibiotics in most chams should be given for several weeks.
The issue I see here is with diagnostics. Baytril is a great antibiotic, but like all antibioitics it only works on specific types of bacteria. Without doing a culture you will not know if baytril is the correct choice. In fact i am not even so sure that what you are looking at is a bacterial infection. What made your vet thinnk a systemic bacterial infection? Did they do blood work? That could be anything from a scar, to retained shed skin, to fungus, or bacteria. Basically anything that can kill tissue and leave necrotic dead tissue behind. The causative agent might not even be present any more and you may just be looking at a scar.