On our pre-assessment/readiness review audit for a combination registration to ISO 9001 & QS-9000, the lead auditor was less than ideal - could not/did not try to understand the main portion of our business and what made it unique versus more common methods of producing metals such as castings, forgings, wrought steels, etc. ( Our primary product is iron powder.) He also was demeaning to our female employees.
I wasn't head of the department, but I would have thrown him off the job after our pre-assessment, and requested a replacement by one of the other well qualified auditors who were part of the pre-assessment team. The decision was made to keep him through the initial assessment. After that was complete, we requested a change to lead auditor to one of the other team members. We also used that same team meember when we upgraded our system to ISO/TS 16949.
There were no issues with having the registrar replace the lead auditor with one of the tem members.