£2500 for a head overhaul does not sound too bad on the face of it by modern standards, particularly as the timing belt and water pump were included in the job, but there's something incomplete about the explanation.
Firstly, where did this errant bolt or nut come from, and how did it enter the engine.
Secondly, if a bolt or nut had found its way into the engine and thereby damaged a valve, the repair would have needed at least one new valve yet there is no mention of new valves on the invoice unless that is what is meant by "cylinder head set".