The similar thing happened to me as well. I can't pinpoint the exact time though, I was mucking around Definance Bay doing quests etc., decided to go back to Caed Nua to delve the megadungeon and was greeted with an unpleasant surprize.
Thankfully, I had one save made before the bug... too bad I'm losing hours of progress if I decide to continue from it, but potential bugs scare me.
Attached is the folder with output log and two saves - the "Caed Nua" one is post-bug, the "Goose and Fox" is the one where all is right:
https://www.dropbox.com/sh/iym4xney4sdeuca/AACYZXyu8vR_TOH-2eIPdreza?dl=0
I hope that helps you in fixing the issue!