Thanks ptrost for the info. Plesk support told me it it does migrate all the mail folders, but then told me to pay for support if I wanted someone to look into why it didnt (apparently you dont qualify for the free 30 days support if you didnt buy your licence direct from Plesk

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callouie, what I ended up doing was used the migration manager to move the sites. Then got those all working first. Note that the migration manager can not handle two cobalt users with the same "full name" if they are site owners.
Then when ready to do the server move I shut down incoming mail on my old server (so as not to have mail going to both servers), and manually moved the spool files and all the user mbox folders. The tricky bit is that you need to convert them from mbox to maildir format.
I did it as follows (from memory, been up all night so if you find a prob, let me know). Note that in these instructions I also redid the mailspool files (which the migration script does do), but as it took time to sort out the migrated sites I left my old server receiving mail, and then redid the spool file once I had stopped my old server receiving incoming mail.
Code:
On new server:
mkdir ~/mailspool
mkdir ~/maildirs
On the raq:
mkdir ~/mailspool
mkdir ~/maildirs
tar zcvf ~/mailspool/mailspool.tar.gz /var/spool/mail/
for each <user> and <user_site> I ran:
tar zcvf ~/maildirs/<user>.tar.gz /home/sites/<user_site>/users/<user>
then:
scp ~/mailspool/mailspool.tar.gz [email][email protected][/email]:~/mailspool
scp ~/maildirs/* [email][email protected][/email]:~/maildirs
On new server:
cd ~/maildirs/mailspool
tar xvfz mailspool.tar.gz
then for each <user> and <user_site> I ran:
rm -rf /var/qmail/mailnames/<user_site>/<user>/Maildir/*
/usr/local/psa/PMM/mb2md.pl -s ~/mailspool/mail/<user> -d /var/qmail/mailnames/<user_site>/<user>/Maildir
mkdir ~/maildirs/<user>
mv <user>.tar.gz ~/maildirs/<user>
cd ~/maildirs/<user>/
tar xvfz <user>.tar.gz
/usr/local/psa/PMM/mb2md.pl -R -s ~/maildirs/<user>/mail -d /var/qmail/mailnames/<user_site>/<user>/Maildir
then:
chown -R popuser:popuser /var/qmail/mailnames/*
service qmail restart
Probably worth scripting this to automate if you need to a lot of users, I dont have so many.
You will need to also tar, scp and move any user sites manually (those in /home/sites/<site>/users/<user>/web), and if you have users that ssh, then any other files they have in their home dir.
Hope it helps.
You'd think Plesk could update their scripts to do all this.
Cheers,
EF