Will my python ever recover?

[Malum Argenteum]

I believe I already mentioned when my vet did bloodwork the time before last, it came back with inclusions on the blood cells. However, the pathologist did not mention inclusions with her most recent bloodwork. My vet told me that it could have been a fluke the first time and to just keep an eye on her. Therefore, I don't really know if she has inclusions or not. For those who don't know, the only treatment for inclusions is euthanasia.

It doesn't look like you did. Six days ago you posted that they could test for inclusions (assume that means PCR testing for arenavirus):

"The supervisor did confirm that she was originally diagnosed with stomatitis. Unfortunately, stomatitis is usually not a primary disease but, is typically the result of another problem. They can also test for the deadly inclusions and nightO viruses."

But the next day you mentioned ruling out IBD

"I believe they diagnosed her with stomatitis due to some inflammation inside her mouth. This was back in October of last year, 5 months ago.

It appears both nidovirus and inclusions are caused from contact with other infected pythons or mites. She certainly doesn't have any neurological or respiratory symptoms so, I think we can rule them both out. Although, there are specific swab tests my vet can do for these viruses."

If a sample came back with inclusion bodies detected in the blood sample, especially in light of the claimed symptoms (and the diagnosed stomatitis, which is the clearest connection), and the vet thought that was a "fluke" I'd get a second independent opinion.

Keep in mind that a snake can test positive for IBD/arenavirus and have symptoms that are not caused by that disease. Many (statistically, most) IBD/arenavirus positive snakes are asymptomatic, and many snakes that are IBD/arenavirus negative can show some weight loss and lethargy caused by many other factors, including age and less than ideal housing (and possibly nutrition as mentioned above, though I myself would start with some B Vitamins).

Euthanasia isn't a treatment; it is an option, though not without a clear diagnosis plus symptoms that support that option. Supportive care is a treatment for IBD (and for idiopathic slow declines).