“The latest update for Outlook 2016, build 16.0.6568.2025, is causing problems for people who use POP3 accounts and have Outlook set to leave mail on the server for a period of time. Instead of deleting the aged mail from the server, it deletes all of the mail.”
It is also a problem if you try to access your email from other devices. It has been a rough 3 days.
For now, I switched my outlook accounts to leave the mail on the server.
When I have some time (haha) I will either switch my POP3 to a IMAP or revert back to an older build of Office 2016.