It is your map that is messed up, right? RunUO uses certian files from the UO client, including the maps. Normally a copy of the client is installed on the server computer to ensure that the required files are present and easily kept current. Reinstalling the UO client on the server computer will replace the map files that the server uses. Just be sure to fully patch to the current osi release after you reinstall.
Do not reinstall RunUO itself, and your world saves will be fine. (A backup never hurts though.)
(edit: waves at ArteGordon
)