Messing around with files in the JSGME backup folder is risky. If you make the wrong changes, chances are you are going to mess up your game folder. The backup folder is made hidden for a reason. To (try to ) prevent trouble.

JSGME doesn't remove files. It only overwrites them, or add them if they are not already placed there.

Best suggestion is to do as Armistead said. Temporarily disable the mod(s) that modified the Umark file. Then pick the original file from the game install folders. And create a new (customizing) mod for JSGME and place the Umark file in it. Re-enable the disabled mods. Finally, enable your customizing mod.

The worst thing that can possibly happen is that you would have to remove all mods (only one, you say - TMO), re-unzip them into your Mods folder, uninstall and reinstall the stock game, then reload TMO with JSGME. As long as you have the original install fileset and the TMO download, you can't break anything that can't be fixed with a little bit of work.

There is software on a PC that only an expert should mess with, like the registry files. Muck them up and you may have to reinstall Windows, which means you have to reinstall every other piece of software on your machine. (Uff da!) That can take days. Even then, you can do all the repairs yourself. But application software is no serious matter. Work carefully. Keep backups. And make sure you have saved the original install package for everything. (You did save everything, didn't you?) Then just wade in and make your mods.

Want to break your computer? Drop it from a height of about three feet onto a hard surface. Only a few other things you can do are likely to cause any permanent damage, and they are not commonly accessible to the novice.

The risk is only one: you can loose an option to properly deactivate a mod, and only if you delete a file from backup folder; if you take a file from there (copy to desktop for example) rename it back to its proper name\extension and paste into game folder - you wont do any harm. But, sure, usually there shouldnt be any need for messing with those files.

JSGME can remove a file: like that: Data\misc\UMark.dds-remove
-but it makes a backup too.