We have these situations happen all the time. It usually becomes a big mess where nobody is getting paid and work sits around for months not completed.
I agree with both Bob and Roger. Resolve any open permits you are involved with. Schedule the inspection and be onsite for the inspection. The inspector should only perform the inspection on the work permitted. In the event other work is taking place or has been completed that was not on the permit application, the inspector should report it to the building department's code enforcement office. He shouldn't confront you or the owner about the issue on the inspection for the permitted work.
He may get some basic details of the issue, but should not be performing an "investigation" or inspection in excess of the permitted work. People do have rights. And if they are breaking the laws, it should go through the proper channels.
