If it cleans mod foobar.esp, it will leave behind a backup foobar~1.esp.
Unfortunately, foobar.esp's date is changed to the current date. This can potentially screw up mod ordering, especially if there are implied ordering rules not explicitly called out in mlox.
Therefore I used the following commands from a DOS prompt (cmd.exe) to assign the modifed dates from all the backup (~1.es?) mods to the cleaned mods:
C:
cd \Morrowind\Data Files
for %1 in (*.esp *.esm) do if exist "%~n1~1%~x1" ctb10w32\touch /r "%~n1~1%~x1" "%1"
Note that this depends on the touch tool found here: http://www.stevemiller.net/apps/
Hope this helps someone.