Sims 4 Mod Manager could actually be part of your problem. It likes to rename files, making it very easy to end up with installation problems and duplicates. I strongly advise against using it.
If you can open Sims when there's nothing in the Mods folder then the issue is something in there. The timing could be coincidence with the changes you made, so it might not be related to the CC you changed. I'd suggest redownloading as much of the content you use as possible from Curseforge or modders' own sites but manage it yourself. Check against Broken/Updated Mods for a selection of mods to not redownload. For the CC, start with the backup files that S4S made.