A couple of things:
Crypto can remain asymptomatic for years. The animal can also suffer from the disease sub-clinically for a long time before noticeable symptoms develop.
Crypto also has some tell tales signs when it reaches the point that the animal cannot hold down a meal. Irritation to the gastric mucosa and swelling which affects the gastric lumen causes the stomach to swell. A proper exotic would be able to note this or even feel it by palpating the middle of the animal. Depending on whether the snake is currently shedding oocysts, crypto can take a couple of cloacal washes to detect.
He could also be suffering from a "lifestyle" disease such as hepatic lipidosis, or even something systemic such as cancer.
I do not understand why the vet would treat him for a bacterial infection. I would have recommended metronidazole or flagyl if I had to blindly deal with a potential protozoal parasite. No I'm not a vet, but I just don't understand the logic of giving baytril or gentamicin for a snake that is not able to keep for down.
I would not offer him another prey item until this is properly diagnosed. The more he eats the more he is going to irritate his digestive system. The root cause needs to be determined before you resume feeding him.
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