You can do it as a single but you'll leave formations sitting on field.
As such they will be sitting ducks as they will sit there till you die, or return and exit.
Its just the way it is, there is no way to rearm the drones. They stay just where they stopped when you landed.
For landing I advise not dropping gear till you are low, slow and actually OVER the runway, drones will dump gear and drop right in. Full flaps and slow they'll hold formation, but once both flaps & gear is out they go into line astern for landing. If you do this a half mile short of base they may end up off the base.
The other option would be once all 3 are down to bail out. Leaving you in the drone 1, bailing out again would put you in drone 2. Where you could rearm and takeoff again.
For a sceneario either the CM is going to have to reopen fields so the bombers can exit and reroll. Or you won't have drones for the second trip.