I upgraded my ispconfig this morning from an admittedly old version and as part of it, now do not see any email in my inbox from before the upgrade. I grepped the files against a subject line that existed before and after the upgrade (new messages this afternoon) and it looks like the new mail is going into /var/vmail/domain.com/user/Maildir/cur now instead of /var/vmail/domain.com/user/cur, so it appears to be a minimal but important change. Based on this, can I just move cur/* into Maildir/cur/* or do I also need to somehow rebuild an index, and if so how would I go about it? I'm relieved that the mail isn't totally gone, but being able to read it would be nice too. I'm not sure if just copying the files will work, or if that will end up breaking things worse.
The different paths that you describe do not depend on the ispconfig version, they depend on the mda and pop3/imap daemon that you use. Courier is using the path /var/vmail/domain.com/user/cur while dovecot is using the path /var/vmail/domain.com/user/Maildir/cur. So the mda type is set under System > Server config > mail in ispconfig. After setting the correct mda and updating this mailbox, you can cpy the newly arrvied files into the existing folders.
Thanks for the quick response. I'm actually fine using dovecot but that did cause me to dig a little more. Just copying the files over and telling dovecot to re-index the mailbox got it done. I have another glitch in that the ispconfig upgrade process caused the server to give 500 errors and fastcgi problems in an otherwise working host so I couldn't convert back to courier if I wanted to, but since I am intending to migrate this to a new server that's just waiting for the files at this point anyway, I won't worry about it.
Your server must be missing some software then, check the matching perfect server guide for your new os version and ensure that all packages are installed.