the picture you posted indicates that you are trying to update a SINGLE mod.
the MOD UPDATER is DESIGNED to UPDATE all the mods in an ENTIRE mods v folder not single mods
the way I update a mod is to place the mod into the mods V folder for the version of sins/entrenchment that the mod WAS RELEASED FOR, then run the mod updater, SELECTING THE ENTIRE mods v folder so that you can see the folders that contain the MOD folders, and after the mod updater has run, I THEN run the manifest maker on EACH of the mods in the 1.041.
harpo