But, I really worry about his functioning and the prognosis attached to this type of infection. Any help or insight would be appreciated. This sounds potentially serious. Minutes or hours, maybe, but not usually days. His doctors were right to think of some underlying cause of the problem.
Viral encephalitis is a reasonable guess.
Treatment with acyclovir for presumed HSV encephalitis is reasonable, since it is a relatively benign drug and the consequences of not treating HSV can be disastrous. The weight loss over the past year makes me think this is not purely viral. Suggest to his doctors that they look into auto-immune diseases such as granulomatous angiitis or limbic encephalitis. This information is provided for your general medical information only. Any specific comment regarding diagnosis, treatment options, and prognosis must come from your doctor after appropriate evaluation.