I've had this problem ever since the RoG release, where if i delete the files while the game is not running and then open up and goto mods, it downloads mods that don't exist anymore?!?!
Problem seems to be with Author Removed Mods and Forum Downloaded Mods.
Since i can't untick the unsubscribe button its a bit difficult for new users to manage.
I know i can go into my subscribed mods in the workshop but unless you know that you HAVE to do that for the ones from Steam Workshop its kinda tricky.
try to use a mod thats been deleted from the steam workshop or from the forum mods, clear the cache and close and reopen the game and goto Mods, or remove the files with windows explorer before launching the game and then load the game and goto Mods.