I will try to clarify. :)
Cut and paste your Mods Folder to your desktop. Run the update. Go into the game and enable mods & cc, exit the game.
A new mods folder will have been generated, but that is ok. Cut and paste your old Mods folder back into the Sims 4 folder, when asked if you want to re-write the Resource.cfg filr say yes. Now you should be able to play the game.