I have Countries Overhaul enabled but every vanilla country still has a core or claim on states which makes it so they can be released so is there a way to remove all those claims/cores without having to go through each .txt file and doing it manually?

Country overhaul should result in all pre-existing claims/controls being removed.

Do you have any other mods enabled which may be affecting things?

No I don't have any other mods

This should now export as you expect