Have you searched the deed records at http://www.alachuaclerk.org/Archive/default.cfm? You may be able to trace what happened to the church that way. It would not assume a black ME church would have become AME.

Look for records on the ME district conferences of that era. They should detail what happened to the church. I would also check other Methodist conference records - AME, CME, UM, etc, and some lesser known African American methodist denominations such as UME, RUME, RMUE, etc.

Also, I would call the oldest African American methodist church in the area, and try to make contact with the historian or eldest members to see what they may know.

Good luck.