In the replay the gear and flaps stay just like they are when you start a replay if you want to see them as they were when you was originally playing then you have to make a flight video.
This appears to be not true. When on final, with all my aircraft, flaps down textbook, gear down, everything looks good.. I land, bring down the spoilers, then retract the flaps as I exit the runway. If suddenly I want to view the landing again, press ALT + O + R, then it brings up the replay screen.. go back 200 some-odd seconds. When it transitions into the replay, all flaps, gears, spoilers, etc. (except the ailerons, elevons, spoilers, elevators) revert to the position they were in at that time; in this case, when on final.
This brings up another point. I don't think it's possible, but could the aircraft your flying determine what you see on the replay? In other words, could there be an add-on aircraft that just doesn't show properly in the replay? (I doubt this..)