Need some help with reinstalling mods after full wipe of my PC.

[FFVIIGod]

So...I had to do a full format on my computer and reinstall everything.

Thought I would be smart and back up all of my mods (for all of my games) onto a portable HDD.

But my PC wouldn't let me do it the way NMM has natively, so I just copied all of my mod containing folders onto the HDD, took me about 3-4 hours (told you I had a lot!) No big deal.

Fast forward to reinstallings. Witcher 3...no problem. Run it, generate the folders, move mods into new Nexus folders and activate. Good to go.

Fallout 4: mods moved over, activate, but NMM is not detecting the .INI file....game still runs though. odd. I fixed this issue, so...yay!

Skyrim OG: No issues here. Easy peasy.

now... Skyrim SE: Got all my mods moved over, game configured, game running like it should. But NONE of the mods will activate. Even if I delete them and Re-install them, they just won't do it!

I CAN run Skyrim SE from NMM, I can access and download mods from Bethesda when in the game. But NMM will NOT activate ANY mods now...

HELP!?!