Either by digging, building the pipe and them cover it with dirt or just dropping trash/rocks/wharever over them to make a ramp so vehicles can get trought, the result is the same, adding a new pipe connection to that pipe deletes all the ground it has on top of it.
I've experienced this as well. Similar trigger, adding a connection to the above ground portion of a partially underground pipe caused all of the fill above it to disappear. I've attached my save file as well as an image of the aftermath.
underground pipe bug.save