Bush League but it almost happened last night

[egj13]

Varsity baseball...5th inning runners at 1st and 2nd, coach makes visit to the mound and replaces pitcher. 3rd base coach calls runners over for a conference during the warm-up pitches. When the warm-ups are completed, runners return to 2nd and 3rd. Plate puts the ball in play and the defensive coach comes screaming out of the dugout that the players were on 1st and 2nd prior to the trip to the mound.

Time is called, crew discusses and runners are returned to 1st and 2nd. So question is this...what is the call if the pitch is (for arguments sake) made, and hit for a double with the runners on 2nd and 3rd scoring before anyone realizes that they went to the wrong bases?