Storage are disconnected from basic rails when their state/direction is changed via logic.
Tested with other players on our server with different carriers : when changing rail direction to undock mining drones (for exemple), the link between the rail and the main storage is always reset. Then you have to reconnect them when the drones are docked again to the carrier to be able to pull their content into the main storage.
(sorry for the bad english, it's been a whole year without proper practice..)