So Orcs get a bonus for conquering unoccupied territories. If the Orcs abandon a territory and then re-conquer it later in a turn, do they get the bonus? Technically they are conquering an unoccupied territory, but should it read "unoccupied at start of the player's turn?"
You have it backwards. Orcs do not gain a bonus for conquering unoccupied territories. From the Rule Book, emphasis mine:
Each not empty Region your Orcs conquered this turn is worth 1 bonus Victory coin, at the end of your turn.
Vacating a territory would mean that it was unoccupied when conquered, and therefore the orcs would not get a bonus.