- Arrive at a store selling DroneCtrl with a bonus Repair drone.
- Go to the main menu and continue, to reload.
- The bonus drone is Defense Mark I.
FTL 1.5.12 added an int value to saved store shelves (after the item id and available bool) that might've been intended to remember this.
In FTL 1.5.13:
- Arrive at a store selling DroneCtrl with a bonus Repair drone. Save.
- I peeked with the saved game editor. That value was 1 (oddly stealth had 2 and clonebay 1).
- Resume the game. Defense I drone is offered instead. Save.
- I peeked again with the editor. All system items had it set to 0.
If that was the purpose of the value (0=Defense, 1=Repair; unknown meaning for other systems), it looks like it's being ignored upon loading and getting a 0 default. In any case, the bonus drone isn't being preserved.