This occured in Pre3, not Pre2, but Pre3 is not an option.

After deploying Pre3, players on my server went to work on something in the Nether for ~12+ hours, and returned to see all villagers in a specific enclosure gone. They were guarded by an iron door, and I've verified that nobody was near them. I had to rollback over 24 hours and manually rollback the individual region file to bring them back, destroying a day of work for several people in the process. They were not pushed out of beds or on chunk borders, the chunks should have not been loaded. The console did not contain any "Wrong location" errors similar to those seen when the chunk issue occured.