Just so I am sure we are both talking about the same thing (because there are a couple other things called Valley Fever) the diagnosis was Coccidioidomycosis?
Best resource for you would probably be the CDC page: http://www.cdc.gov/features/valleyfever/
University of Arizona also has a decent page: https://www.vfce.arizona.edu/ValleyFeverInPets/
As I said, I do not have first hand experience with the infection in dogs and it has been quite some time since I have done any pathogenic fungi work. That said, the information I can offer you is not much more than the above pages can provide. It is a fungal infection that is sometimes self-limiting but other times requires treatment. Because it is a fungal infection it can be difficult to treat and the treatment course tends to be extended. There is a fairly high incidence of relapse and usually treatment of a relapse is even longer than initial treatment. Some relapses become chronic persistent and will require lifetime treatment.
Based on what you have said it sounds as if your dog may have had a relapse. I would discuss with this possibility with your vet and if he agrees that that is the case and you need to begin treatment again I would advocate using a different anti-fungal than the one used in the first treatment (that way you avoid the chance of creating a resistant strain).
Your vet should be able to offer you good options on prognosis and treatment.
I hope the best for you