do I have a case? with nothing in writing will the courts believe me?
So put it in writing. Send Santander a letter explaining what has happened with as much detail as possible about the phone conversations. If Santander just say (as they probably will, unless they just ignore the letter) that they have no record of the agreement, then that is their poor record keeping that is to blame. If Santander say that there is no such agreement (they are unlikely to say this if they know that you are in the right), then you are not in a strong situation. The letter could state that you will be taking legal action if payment is not made within 30 days. It should state that the balance showing on the account, being made up of unreasonable charges, is disputed.
You should keep a copy of the letter and posting receipt (or use recorded delivery).
One option, other than taking legal action yourself, is to ask Santander to take the debt to court as soon as they can. Then you can put in a counterclaim. This course of action would be appropriate if the money that you've overpaid is small in relation to the charges that Santander are asking from you.