sims 4 cc will not delete

Which file do you mean ? The cc one ?

Both my Mods folder and the entire Sims 4 file 

Sims 4 file ? You mean the folder in documents ? It recreates but your mods should no longer be there when you rename that folder.

Are you using oneDrive or any other cloud services ?

Yes, but when it remade the folder the Mods folder was empty. However, all my cc was still showing up in the game. I'm not using any cloud services

Try the following

Create a new Sim and save that to your library

Then go to your tray folder and see if there's any new files appearing there.

If not, the game is using a different folder than the one you renamed.

That's what I thought, but I have searched my computer and there is only 1 folder. 

Did you try above suggestion ?