Something else I found!
After finishing act 2 and at the first reincarnation, my total years went from 1420 to 1377, as I did some testing with a earlier save. That also comes back when you do another investigation, and so it was 1430 to 1387. The time its eaten seems to be the same, so I figure its either intended or a small bug.
After a bit more testing, its always at the first reincarnation that it seems to trigger the loss of longevity. If you finish a investigation that gives some longevity, it does put it back, but at reincarnation it is lost.
Edit: Did more testing, this time I got the dead tide investigation done, which got me 20 years. So it recovered the 1377 to 1440, and then on reincarnation it went to 1397. Maybe something inst getting counted right?