I get this kinda of work in all the time where the owner/operator played repairman and did more damage than repairs.
This where some of us may differ on charges. I warranty my work and I am glad to rework things when needed but when the customer decides to disassemble things prior to returning the item for warranty repairs I sharpen my pencil as I charge for reassembly and missing parts. It is work a lot times that is unnecessary just to troubleshoot the complaint problem. I do repair what was originally the problem plus parts if a repair item of if the whole unit I sold then no charge for the work that would been needed before the customer decided he more about it then the repair shop.
Some customers will complain about the costs even when it is a complete reassembly project like the fellow that brought in a riding mower that had a bad steering shaft bushing. What I got in was a pickup truck load of boxes and the mower frame. He complained to high heaven because I felt sorry for him and only charge him $50 plus parts to do a 2 day job. If he had just brought the mower in it would have been a 30 minute job. He just kept complaining so I said I could rework the bill and charge for the 16 hours of labor; he shut up... I haven't seen him since but who needs a customer that wants everything done for free including new parts.