Hello,
I see this topic is almost a year old, but I have the samme issue and have found no fix for it.
Here are all the relevant files: https://www.dropbox.com/s/5y3vi67tgc09vbu/Pillars%20of%20Eternity%20zone%20reset%20bug.zip?dl=0
Unfortunately, I have no later save that does not have the bug, but they're only 5 hours of game time apart, and one of the only things I did inbetween were Heritage Hill and the Ondra's Gift lighthouse.