Just ran into this bug today. In the midst of a rearrangement, I noticed my spawn points were increasingly erratic and random (sometimes out of bounds or in rooms that were in the middle of construction/deconstruction). I decided to try changing which hall was the spawn point. Changed it to a different one, then reverted back to the original one (starter hall). After that, all my transporters disappeared. Built a test one to see where they all ended up, and most of them were out of bounds. I was able to recover two, but some others I had to remove and rebuild. I'm peeved about this last point, as I rushed most of these transporters' builds. Would love to see a fix or a workaround.
There are currently 3 transporters still broken that I can't access to remove or return to their original locations.