I'm not sure what you mean by 'linking to middle of room'? Can you elaborate? If the room was not in the list, then the layout editor thought it was being drawn- that's not good. If you are able to duplicate it, the exact steps taken would be helpful.
Yeah, sure thing. I've been able to reproduce it on the first attempt with a brand new game. This is what I did:
1. Opened the room layout tool immediately after creating the new game from the template.
2. Placed six new room boxes named Logic 2 to 7, arranging them in a 3 x 2 arrangement.
3. Linked them using bidirection links.
4. Closed the Layout tool
5. Right clicked on "Logic 3" and selected Remove from game.
6. Opened up the Layout tool again. At this point I saw the unattached links with the red triangle pointing towards where the Logic 3 box had previously been.
7. Right clicked on each of these unattached "error" links and deleted them.
8. Added a new Room box again and chose "Logic 3" and the same logic number as the one I had removed from the game.
9. Attempted to create a bidirectional link from one of the other rooms to the new "Logic 3" box. This is where I end up with the unidirectional arrow pointing to the middle of the new room box (see attached image below).
10. I then right clicked on that blue arrow and chose to delete it. Both the "Logic 3" room box and the blue arrow disappeared but the "Logic 3" logic is still showing in the resource list.
11. I then closed the Layout tool and reopened it. "Logic 3" room is still missing (see second image attached below).
12. I then select Repair Layout and the "Logic 3" room reappears. This time I'm able to recreate the bidirectional arrows from "Logic 2" and "Logic 5" without any issues.