Actually loosing drones is by design. Bot does not dock drones if it detects scrambling NPCs in < 20km. If distance > 20km bot send dock drones command but do not wait while drones docked. My idea was if bot dock drones while NPCs present, NPCs may reaggro to ship. Also if ship already scrambled, fighting drones may help to kill NPC while bot trying to warp out.
I added new checkbox to always dock drones (in
beta version). If you tick it, bot will send dock drones command even if scrambling NPCs closer 20km. Bot will still not wait for drones. If this is not enough, we will add timeout to dock drones.