Observations :

Recent reported instances of POP accounts facing compatibility problems with Outlook 2016 wherein users have configured pop in Outlook 2016 version & enabled “Leave a Copy on Server” – yet mails were getting deleted from server/web mail.

• User found mails from webmail were getting deleted
• Receiving Duplicate mails in Inbox in Outlook 2016

Cause :

On further research this was found to be a problem specific with users of Outlook 2016.
Microsoft Outlook 2016 has an identified bug Please refer to their Forum

Solution / Workaround :

Microsoft in their forum above have suggested a workaround & you can also be further updated on the status of this bug fix by visting same.