Email Troubleshooting: Emails Suddenly Disappearing
There are several possibilities as to why your emails seem to have suddenly disappeared:
It's possible that someone logged in and deleted or moved your emails or that your email filters have moved them. Check your other folders, especially Spam and Trash.
A POP3 configuration means your email will be stored locally in the email application you're using to access your mail on your computer or mobile device instead of an IMAP configuration where your emails are stored on the server. If you've set up multiple email applications (such as Outlook or Mail), your emails may have been downloaded to one of your other devices.
To prevent this from happening, be sure to set your POP3 account to leave copies of messages on your server. In Outlook, this is found at Tools > Accounts > Edit the email account > More Settings > Advanced > check box for Leave a copy of messages on the server.
This mistake is much more common than you think. Be sure you are using your full email address for the user name when you log in. If you put your cPanel username, you will be in the wrong place.
Again, the user name you log in with must be an entire email address, like firstname.lastname@example.org. If you are not putting the @example.com part, then you will not see the correct inbox.
Some scripts, by default, use POP3 to retrieve emails from the server. It is recommended to use IMAP for retrieving your emails. You will need to consult your developer regarding the said script's setup and/or configuration(s).