I think for starters I'd locate the actual reasoning and do a bit of an investigation. You need to determine if he was properly informed of they repair and the cost (in accordance with your policies), and if there isn't any evidence to suggest a issue with your employees - side with the employees.
More often than not, the customer found another shop that'll do the work cheaper.
I'd offer some type of "consolation " prize to the customer - a discount on completing the job or allowing the parts to be returned and customer pays the original labor quote to reassemble the vehicle and the shop accepts no liability.
Obviously don't give the farm away, but if he feels cheated try and help within reason.
I think it would be extremely rare to have a situation where the staff is at fault. They could have possibly set better expectations or communicated cost and job description better, but I doubt that's the actual cause of this situation. If it is, unfortunately the right thing to do is return the parts and eat the labor or come to modified agreement in regard to the customers concern with fixing the vehicle.
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