On a route check the captain under check is the PIC. There is no authority for the checker to boot the operating captain out of the seat. I can't envisage a circumstance where this would even raise itself as an issue.
There is an exception where the checker is the PIC if the captain under check has an 'expired' route check. He is the PIC from the back seat and technically could boot the checkee out of the seat but even in a situation such as this I would find that incredibly unlikely.