If you are sure that it was not a miscommunication and misunderstanding issue, you can try several ways to get the money back:
1. Write a letter to the manager of the store (also submit online through contact us).
2. Write a letter to the manager of the regional office if you can find it online.
3. If you paid by credit card, dispute this via your credit card company through the website or send the letter.
4. Submit the complaint to the Better Business Bureau through the webpage. They will pass it to the store for an answer.
Most of the time it should work, not always though. Basically, no need to talk in person or call because these waste time. Writing is the best solution. You should be able to do all the above in one hour.
The bottom line, even if you did not get the money back, it is fair that they charge you the diagnostic fee because that is basically the routine practice of all garages and the diagnostic process takes time. Applying diagnostic fee to repair fee would be a grace.