you can not overwrite, you can not delete to uninstall, you must use the uninstaller the mods creates to completely uninstall.
but it sounds like it is too late at this point.
this may be difficult for you then, but just follow directions below.
open "regedit.exe" in C:\windows folder.
find HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Microprose\Star Trek: UM5 (64 Bit systems)
find HKEY_LOCAL_MACHINE\SOFTWARE\Microprose\Star Trek: UM5 (32 Bit systems)
select the "Star Trek: UM5" folder on left and right click, from menu select delete and confirm deletion.
note; you may need to run regedit.exe as administrator
then all in one will install UM5