We have heard reports from multiple POP3 users at different locations that Outlook 2016 is permanently deleting messages off the server, seemingly overriding their Outlook settings to save copies of messages on the server for a specified number of days or until deleted from Outlook. Some of these same users are also reporting duplicates of messages.
It appears that the bug is limited to Outlook 2016. There is no resolution at this point in time from Microsoft. Our recommendation is for users to revert from Outlook 2016 to Outlook 2013.
Apparently Microsoft is escalating the issue and presumably a patch will be issued.
As we learn more, we will follow up with clients who have contacted us about this issue.