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It did say in the TES5Edit walkthrough video that newer versions may do something similar to this in the annotations.
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I'm using the latest Mod Organizer (v1.3.8, non-beta), the latest TES5Edit, and a couple other things that I don't think affect this particular process. If I remove the duplicate backup.esm from the Overwrite folder, it removes the entire backup.esm option from Mod Organizer itself and comes up with a different alert (Missing Masters - no guided fix), as it's not present anymore. I copied the duplicate(?) update.esm into a backup folder, and also left it in the Overwrite folder. I want to do all this flawlessly the first time so I don't have to redo entire portions of the mod utilities+installation process, but I don't know how to proceed. you can double-click on Overwrite and drag the relevant files into the mod. Mod Organizer had an alert in the top right (!) (There are files in your overwrite mod) (No guided fix). Mod Organizer does not currently support. but in the Overwrite mod directory I ended up with both the backup folder with the backup update.esm in it as seen in the video, AND an additional update.esm directly in the Overwrite folder which I didn't intentionally create, and I have no idea if it's the original or cleaned version :/
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