Since I posted the same thing yesterday in the bug reports: the update.esm in your skyrim folder should now be smaller than the one you backed up. Do the following:
1. Go to your MO mods folder (you find the location in MO's Settings -> Common -> Mod Directory, loose translation from the autoenabled translation in my version) 2. Create a new directory, e.g. "STEP Cleaned Update" 3. Move the smaller update.esm from your Skyrim\Data directory into the new directory 4. Move your backed up file into your Skyrim\Data directory 5. Restart Mod Organizer
You will now have the new mod listed, just as if you had created it according to the current docs.