Duplicate Emails Microsoft has reported an issue with duplicate emails when using "Microsoft Outlook 2016" as an email client and configured to download your email via POP3. The symptoms you may experience are the following:
After Outlook downloads your email, all the email messages on the server are deleted from the Inbox in webmail.
Email messages are downloaded multiple times in Outlook, causing duplicate items. We have identified that this is not an issue with our mail server and is a bug in the latest update of Microsoft Outlook 2016.
You may refer to Microsoft's link below which will give you further information regarding the issue and also update once this matter has been resolved.