Mod Manager not keeping some 3rd party mods "active"

This issue has so many complex sidenotes, I'm not even sure where to begin. I'll just simply say that there are certain 3rd party maps/levels that if I activate the mod, play it, then close game, then reopen game, go into mod manager again, it's been deactivated again -- without my doing so.

Doesn't do it on all, but I've noted it on Roane Co. Tennessee, Southern Hwy, CrashHard 2.0.
Ironically, ECU lighted, and WCU lighted, do the opposite. I deactivate them, close game, open game back up, and they're re-activated without my doing.

So point being, the mod manager has a mind of its own and seems to activate and deactivate my stuff willie-nillie. Anyone else having this issue?

Also, having issues with changes made no longer being recognized by my Documents/BeamNG folder in my separate F-drive external harddrive-- such as levels I've saved in the world Editor. I have a feeling this is related to the article I read on v0.22 and up having a different file structure-- which okay, maybe makes sense...

... but unfortunately I tried to read that thing twice/three times, and it made absolutely no sense to me.
What exactly is different now-- that isn't as simple as C\Documents\BeamNGDrive\etc. etc? (or in my case F-drive and everything else thereafter?

I transferred some files to Appdata\local\something or other... and others to F\Documents\0.22.1.

I have multiple duplicate files all over the place, and have no idea what's what anymore.

Do I need to delete all my files and do a complete re-install from Steam to get this working right again?
Should I only be running this off the C-drive and not telling it to go to an external harddrive?