Last night on my debug build I was moving around the world and just going up and down staircases, saving and reloading occasionally, to try to recreate the bug, but I couldn't get it to happen. This weekend I want to write a new test that will do the same thing automatically, and then just leave it running until something breaks.
I've also tried actually deleting level files when I was on a different level in game, and I do get the same result that the portals can't relink if a level is regenerated. I'll try to at least get that to work.
If you still have save files where this has happened, can you please send so I can study what happened? I might be able to get the areas unblocked too.