It will count if the examiner agrees and signs it off - which I imagine he would.
It is not perhaps widely appreciated though that the 'hour with an instructor' can be replaced by any other skill test or proficiency check, for IR, class or type rating, or for the IMC rating. It doesn't have to be on an SEP, doesn't have to be an hour long, doesn't even have to be on an aircraft (sim for LPC counts).