After changing the SPAM filtering to "not filtered" for one of the domains it disappeared from the management interface. The /var/vmail/<domain> directory appears empty but logging into the webmail interface with an active user still shows all emails, even after reboot. Is there a way to recover from this?
Which software do you use? You posted in the general Linux questions section and not the ISPConfig section, so I must assume you are not talking about ISPConfig here.
Ok, I've moved your post to the ISPConfig forum. Dovecot accesses emails from /var/vmail and webmail connects to dovecot via IMAP protocol. So I do not see any way how it can be possible that /var/vmail/<domain> is empty but webmail still shows the emails, from altering the policy, please double-check that. My guess is that you accidentally did something else. Maybe you renamed the email domain or something similar. Have a look at Monitor > Datalog History, there you can see what exactly has been altered with that change. Or maybe you altered the mail root directory under System > Server config some time ago and the change got just applied now when you changed the policy, so also check that the the filed: Maildir path = /var/vmail/[domain]/[localpart] Homedir path = /var/vmail under System > server config > mail.