So, I had to close the game mid mission, right after Boiling Point when Lambs to the slaughter started.
And now every freeplay target with some few exceptions on the countryside is back.

The dots marking them are still gone and I don't get any contraband for destroying them, but they are back and haunt the freeplay. It's very frustrating to see everything you've cleared to be cluttered with Nazis again. Even the bridges are back. Is there a story reason or did the game just completely bug out? I assume it's the latter.