If server1 use "file1" and server2 uses a different "file1"(checksum calculation) you will get the message version mismatch if you join server2 for example.
When joining server1 "file1" will me loaded into memory and can not be purged from memory unless you restart ut2004 again.
If you still have a version mismatch, then you probably installed/copied the file manually in to the ut2004 map (map, u file, texture etc.) and you need to remove this mismatch file it manually for UT2004 load the correct file when joining the server.