The mail for an individual cPanel account is stored in /home/$username/mail/$domain/$mailbox/, while metadata for the account (mailbox passwords and quotas) is stored in /home/$username/etc/$domain/.
For migrating a full domain to another account or server, copying these two folders and fixing their ownerships is sufficient to enact the migration. In addition, there are a few bonus files to look at:
/home/$username/.autorespond*/home/$username/.spamassassin*/home/$username/.sqmail*/home/$username/.cphorde//etc/valiases/$domain
These are, respectively, autoresponders, SpamAssassin settings, SquirrelMail settings, horde settings, and forwarders. Each of these metadata files will add to the completeness of your mail migration, making a smoother experience for the clients when they start using the new server.
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