You can take my game… when you pry my cold, dead fingers off the board!
The rules say to remove a space lane
to a system that is only connected to one space lane system and is not in use.
-When in the turn sequence do you remove the space lane?
as soon as it happens, i.e. as soon as a ship leaves the space lane empty.
-Does this potentially create a bunch of systems that aren't connected to any space lanes at all?
-Can another player, snatch the un-connected but explored system and connect it up to a new space lane half way across the board?
No, these can't happen. You only remove empty space lanes that extend from a single system, connecting to nothing.
So a space lane with a system on both sides would never be removed.
Edited your rule quote above to be more accurate. Perhaps that is where the confusion lies. Check pg 12 again.