Have you tried using something like Heritage Quest and doing a "loose" search. Possibly surname with approximate birthdate but no given name or just first initial of given name? Also, on Gedmatch have you searched other gedcoms for possible clues using different spelling or tried following trees of siblings he may have had? I like rootsweb for entering surname, location, but add birthdate with +/- 10 years to find possible siblings or to find him listed with family. Using user look up from gedcoms you can find Gedmatch #'s and do one-to-ones.
I once did a search on a line where the person moved to another state in an adjacent county and changed his name to end in ee instead of ey because he was wanted for selling liquor on a reservation. He told those searching for him they were confused because he spelled his name differently.
The only other idea would be (depending on generational distiance) to find anyone with that surname who have Gedmatch numbers and try running a series of one-to-one comparisons. I have gone through Wikitree finding people with common surnames as those in my line and running one-to-ones. Have come up with a few matches.
If he died, have you done any funeral home searches in the area he was last known to live in the time frame he disappeared? He could have been buried in unmarked paupers grave but if no money, the funeral home may have been paid by the county or a church and may have a record.
