For anyone else who likes to backup their files. Make sure you don't copy a "copy" of your Data/mods folder to the game folder itself. Keep your "/data/mods" folder separate from the folder containing "SkyrimSE.exe" file and let Vortex do the manual work of installing folders and such. Again, don't manually copy and paste a folder to the NEW drive the game is installed on from a previous drive if you copy a backup folder of steam files and games to paste to the NEW drive. *Hopefully that makes sense*
A lot of trial and error with this (new to me) issue, thankfully I didn't lose anything. Hopefully the next person who reads this error post, *should they run into the same issue*, can happily go back to playing Skyrim.
