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I am not sure what triggered it but all of my Lunden mysteries are gone. They do not show on the map and going to the locations does not activate them. I loaded an older save (2 hours old) and the mysteries are there so it looks like some sort of corrupted save issue as all of my recent autosaves have the issue of the missing mysteries.
Closing and reloading the game did not help.
I can see mysteries in all other zones and it looks like only the Lunden ones are missing (the zone I was playing in at the time).
Oddly enough the game did crash right around the time I noticed this, but it crashed while I was looking at the map to go do one of the mysteries and noticed it was not there so I am guessing that they were gone before the crash.
I do not want to keep playing and find out I am screwed but I also do not want to go back 2 hours and redo a bunch of work. Pretty bad bug to show up after the game has been out for a year.
EDIT: I was pretty sure that with the Christmas holidays I was not going to get many responses to this issue so I went ahead and loaded my old save to see if I could progress with the mysteries. I found that after taking the "Smashing the Compass" quest the mysteries were no longer active. After completing that quest it looks like the mysteries reappear. I hope this helps someone in the future save a bit of time and frustration.