You may find that the term "deserted" as found in records for Confederate soldiers is somewhat ambiguous. The real possibility is that your ancestor got tired of the unit he was in and just took off, linking up with a unit that he liked better, or maybe he had friends there. This happened quite often. Confederate soldiers were very independant and not prone to very willingly subject themselves to authority. Perhaps the 65th Inf. was a bit more diciplinary than the 11th Cav. Who knows. I believe it would be helpful to obtain his records. Even if you don't find out anything new, you will still have those documents. They are available on this site.