Unsubscribe from the mods you wish, then go into the mods directory and delete the mods you unsubscribed from.
There's a guide online on how to completely clean all of your addons on Garry's Mod, I assume the same applies on any game instead of getting you the link I'll just tell you, it's rather simple. Sort of like a website cookie, but for Steam.
Its name is The Binding of Isaac: Afterbirth and it hints us about the famous chapter about Abraham and his. Cracked Binding Of Isaac Mods Without Steam.
If you have files missing you'll want to varify the integrity of your game cache.
