If a customer happens to delete their emails you can still retrieve them from the cpanel backup system. This will take root access to move the files from the backup folder tot he customers account.
You can extract a backup archive and copy over the emails to an account’s existing mail directory. If restoring a backup archive, you will find emails located at:
You can also find emails from the default account within:
The following thread is intended for manual migrations to cPanel, but it includes details about the maildir structure that will be useful to you: