I guess you have to decide honestly if the parts replaced were fitted due to sound diagnostic reasons or as a best guess situation. You could always remove the new parts & refit the old stuff & keep them in "stock" as test devices (We all have them).
Your situation with the company that tested the injectors is a separate issue to the situation between you & your customer. I would make sure your customer is treated as you would expect to be treated by a supplier. You can then speak to the testing company.
Some items are difficult to get tested / reconditioned properly. I know of a company that apparently reconditions Injectors but don't supply a new coding number (when applicable) saying to use the original coding number on the injector.
Steve