After looking at 131868 i would say it is at least related, especially to the second version of the problem, which is the alternative discussed in that thread.

What did you do?
In map view I dragged the ghost belt over the following belt assembly, from top to bottom.
Before.png

What happened?
It was updated to the following result, and the underground belt at the bottom was deleted (removed from the game/not marked for deconstruction). In character ...