It's more likely that deleting your documents folder erased the files and had the game rebuild them. Let be try to be a bit more specific:
When I install mods, they will normally install into the game's mod folder. Some, however, will edit, add, or overwrite actual game files. These changes could be made to files in the installation directory, to config files in the ...\Documents\The Witcher 3\... folder, or saved to "virtual directories" if that's the method that your mod manager uses. (Not sure what the case is, because I don't know exactly what you've done over time.)
However, since the game was working before, and it's not now -- something definitely changed. Since you're seeing it in a new game, but you have not reinstalled the game since using mods, then the change is likely due to something left over from the mods that the game is expecting to find, but is no longer available.
Most likely suspect: there was something leftover from the mods in your Documents folder, and it was either deleted or the pathing to it was broken in the little update / reversion you're describing. Have you tried starting a new game since the problem first arose?
Best potential solution: a.) Uninstall and delete all references to the prior installation. b.) Manually clean out files and folders that may indirectly affect a new installation (like leftover folders and mod managers). c.) Install the game again to a brand new, never-before used installation path. In that order -- very important. That will ensure that Windows has to rebuild the game data in a 100% vanilla state, and any third-party data that may be affecting the old path will no longer be able to find it.
Now, if that doesn't have an effect, we can be fairly sure that something in your actual system has become affected. This would not be the fate I would choose.
