I recently ran into this problem when our anti-SPAM measures changed. Our qmail email server was bombarded by SPAM and our user’s inboxes filled up. If I connected via IMAP and deleted a lot of messages, the $HOME error went away.
Another method I found at POP3: unable to scan $HOME/Maildir? was to to increase the softlimit for pop3d which is found in your pop3d run script such as /var/qmail/service/pop3d/run (for e.g.): Set softlimit -m 2000000 to higher value.