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If you are using POP3 connection through Outlook or other similar mail client, then it is possible that the emails were downloaded to your local system, try checking your mail client in your computer to find the emails. If you set your POP3 account to leave email copies in your server, then this will not happen.

There is a bug in MS Outlook 2016 that deletes messages from the server in POP accounts even when set to “leave messages on server”. Please see the following link for more information:

https://support.microsoft.com/en-us/kb/3145116

Another problem is accessing wrong account. Make sure you type the entire email address like this me@domain.com. If you leave the @domain.com part then you will end up in the wrong inbox.