That's a tough spot. It's understandable that he just couldn't figure it out. I think we've all been there. We thought we knew the problem, but it turned out it was something else, or something that we couldn't figure out. I would expect to still pay, but I would expect it to be a reduced rate.
I can actually give an example of this. Currently have a subcontract job here at the shop. We got called out to a location about 45 minutes away to replace lights in a parking lot. This is not normally something we handle, but we've worked with this company on other sign stuff, so we agreed to take the job. Got there, got the parts needed, replaced them, and it didn't work. Service tech spent half a day at the location and talking with the local electrical supply company. Turns out they actually purchased the original fixtures for the lights, and they were covered by warranty. Replacement parts ordered. Waited two weeks, went back, new parts still didn't work. Contacted manufacturer again, they're shipping out whole new fixtures.
We're paying nothing for parts because of warranty. And we're charging a reduced rate on the installation. It's not our or the client's fault that this is a crazy situation. We're charging for the time spent in travel and up in the bucket. Not for the leg work with the electric supply company and the manufacturer.