I will tell you what I have heard about those folks who moved the Confederates.
They were "not the highest kind of folks", so it is very possible he was moved and is
with the Union folks, but is in a grave marked "unknown USA."
All kinds of things could have come up so 1) there could have been a rain, 2)the markings could have been
washed away, 3)they stopped for a lunch break and forgot to put his name on his box, etc.
If it is important to you that this man have a marked spot, I would suggest he
have a memorial stone with his kin people, where ever they may have been laid to rest.
Wishing you the best with this search.