I have had similar issues every time when starting the game for about a month now. I didn't do anything to my PC though (that I know of), so it came out of the blue. In my case, none of the mods or cc are actually broken/corrupt but for some reason, the game won't start with all of them. I have to remove the entire folder, open the game, close it, add a few mods/cc at a time and open the game each time in between. Yes, every. single. time!
Whenever it is a mod or cc that's causing a problem that pop-up message always includes the exact file(s) and location, so the general "it's-a-problem" ones have never been due to actual mods/cc or missing files for me.
It's really tedious, but if the game won't start at all and you can't seem to narrow down what mod/cc is causing it, it might be worth a try since it's entirely possible it's not the mods/ccs fault. I have 5002 files in total with maybe 10 being actual mods and the rest cc, which sounds like a lot but my PC should have no issues running them all and, as I said, they do if I start the game over and over adding a few at a time. I'll assume yours are powerful enough to do the same.
Idk if it's remotely the same issue but that's what I do for now while trying to find a solution that doesn't include having to trash and redownload 5000 mods/cc. Hope you get it sorted without having to sacrifice your mods and cc 🙂
