This would seem to be a logical screen flag to have. That way, you can make difficult enemy rooms that don't come back once cleared. You can also have sub-boss rooms with additional enemies, and when cleared, none of the enemies return.
On a related note, it would also be cool to have the option of having boss-type enemies like Aquamentus return once defeated (another screen flag?)
Just some suggestions for the developers and other members to ponder.