This is fixed in build 16.0.6568.2036. To get the update manually, go to File > Office Account > Update Options > Update Now. Note that after installing the update, you may need to let Outlook download all POP3 mail one last time.
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. Ouch.
Until this problem is fixed, there is a simple workaround: users can uncheck the option to delete mail after a period of days, while leaving the "leave on server' setting checked. This will leave all email on the server for a few weeks, until the problem is fixed. To do this, go to File, Account Settings, double click on the POP account then click More Settings. The leave on server setting is on the Advanced tab. Untick the option to delete it after a specific number of days.
If it were only that easy... there is second issue with this update and POP3 accounts. POP3 mail left on the server keeps downloading, over and over. The usual fix when this happens is to not leave mail in the Inbox on the server, however, this won’t help someone who wants to leave mail on the server.
Switching to IMAP will solve this problem, but because there may be other issues, I recommend reverting to an older version and waiting for the next update.
To revert to an older build of Office 2016, first, go to File, Office Account, Update Options and Disable Updates then create an appointment on your calendar to re-enable updates in early to mid April.
Open a command prompt as Administrator. In Windows 10 or 8.1, right click on the Start button and choose Command Prompt (Admin) then type or paste (right click in the command prompt screen) this command line to revert to the February 9 2016 build 16.0.6366.2068 (it's all on one line - make sure you use the leading double quote "):
"C:\Program Files\Common Files\microsoft shared\ClickToRun\officec2rclient.exe" /update user updatetoversion=16.0.6366.2068
It'll take a few minutes (or more - possibly about as long as it took to install Office) to update the installation and you may need to reboot your computer.