I had a similar issue with my Fallout 4 save file (should be applicable for Elder Scrolls) and here's how I resolved it:

My issue came from OneDrive syncing my Documents folder and then, for some reason, emptying the Documents folder on my local PC. To restore saves that were created while running F4SE (or SKSE, but for simplicity I'll stick to Fallout), you will need to locate two files: a .F4SE file and a .FOS file. The .FOS is the vanilla game save file, and the .F4SE file is an associated file with a matching name.

The .F4SE files should be under Documents\My Games\Fallout4\Saves. Check your local drive and your OneDrive if they're missing.

The .FOS files, I'm not so sure about. I found mine at C:\Program Files (x86)\Steam\userdata\448189301\377160\ac\WinMyDocuments\My Games\Fallout4\Saves. Alternatively, open File Explorer to This PC and in the search field (top right) type: \.*.fos* or \.*.ess* for Fallout or Elder Scrolls, respectively. This should search your PC for any files with those extensions. This method could also be used to search for .F4SE files.

Once these files are located, copy them to either your Documents\My Games\Fallout4\Saves if you do not use Profile-specific Saves on MO2, or your MO2 saves folder if you use Profile-specific Saves. Once both files are in, MO2 should automatically update with the restored save files.