Why can I see my email files from File Manager, but Webmail does not show them?
Dovecot reads from its index files when it displays emails in webmail. The issue that webmail exhibits in this case may be caused by a corrupted Dovecot Index Cache. To address this, you can remove the Dovecot Index files with:
/scripts/remove_dovecot_index_files --user cpuser
Replacing "cpuser" with your username. In doing so will remove the current Dovecot Index files, and then refreshing webmail will regenerate them.