This can happen if the email box was deleted in the control panel and then added back, or the account was deleted and then re-added. Depending on whether the emails in sent, drafts, and junk are new, this could have occurred.
Otherwise, messages can be deleted inadvertently if an email client has the option set to delete all messages on the server. Thus if someone had selected this option in a program like Outlook and checked the email box, messages would no longer appear in their webmail inbox.
If you have root access to the VPS, then you can review the mail server logs. For Exim with cPanel, this should help: View Exim Mail Activity
Here's how to
grep a single email address in the logs: Grep / Search the Exim Mail Logs
If the account, email box, or messages were deleted and you're backing up on a daily basis (as you should do), you can try to restore the account. Just be sure to do an account backup prior to doing this, so that you won't lose anything new since the backup was done.
For this, and for additional help retrieving emails back into the email account, you should contact cPanel's tech support if you have a license with them, or your web hosting company if not.