When you login to your account via ftp, you'll want to stay outside of your public_html directory. You'll see a folder called "mail"

Inside of that folder, you'll see other folders for all of your subdomains, etc.

However, there is one file in there called "inbox". It has no ext. You can delete this (it will be recreated as an empty file, the next time you get mail).

The alternative is to open your email client (Outlook, etc), check mail on that account by creating a new email account in Outlook, with your cpanel username@domain, and cpanel password.

It will then check that account as it does your others.

Note: I was shocked one day when we decided to check the account as a regular account for the first time, and received 23000 emails.