Found it.
Chapter Approved 2017, p67.
"You cannot use the Command Re-rool Stratagem to affect Mission dice rolls. Mission dice rolls include any dice rolls that are made before the battle begins (such as those that determine who chooses deployment zones or who gets the first turn, those that must be made at the end of a battle round (such as rolls that determine if the battle end) or any rolls that determine how many victory points are awarded to a player."