RC Transport Underground

o/

So, I'm feeling a bit dumb at the moment, so I have to ask.

In short, I went underground to clear out the discoverables and then ship out all the resources.
At first I managed to get my RC Transports to automatically go out into the caves and haul back to stockpiles, but then I wanted to get the resources to the surface so I grabbed the Transports to ship some of them up the elevator. This seemingly broke the automated behaviour? No matter what I do, even restarting the game, I can't get them to be automated again..

Is there any way to get them hauling again? Or is there some better method of clearing out the caves and getting the resources to the surface?
It's my first playthrough, and playing Relaunched (if it matters).