This is fixed in build 16.0.6568.2036. To get the update manually, go to File > Office Account > Update Options > Update Now.
The February 2016 update for Outlook 2016 is causing problems for POP3 users. Build 16.0.6568.2025 is causing problems for people who 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, users should 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. 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.
The second issue with this update is that POP3 mail left on the server keeps downloading, over and over. Although I'm not sure exactly why it's downloading the mail multiple times, the usual fix when this happens is to not leave mail in the Inbox on the server. That won’t help someone who wants to leave mail on the server.
Switching to IMAP will solve this problem, but you might want to revert to an older version and wait for the next update.
Revert to an Older Build
First, go to File, Office Account, Update Options and Disable updates then create an appointment on your calendar to re-enable updates in early April.
To revert to the February 9 2016 build 16.0.6366.2068, open a command prompt as Administrator and type or paste this command line in the Command Prompt window:
"C:\Program Files\Common Files\microsoft shared\ClickToRun\officec2rclient.exe" /update user updatetoversion=16.0.6366.2068
Look up the version numbers at Version numbers of update branches for Office 365 clients
Published February 24, 2016. Last reviewed on March 5, 2016.