I'm a little confused now. In a traditional Split Domain migration you would have users for the same email domain (let's say domain.com) spread out over two servers (perhaps more) - say old-server.domain.com and zimbra.domain.com. Once you migrated all the users off of old-server.domain.com you are ready to make zimbra.domain.com you're primary server. You would then reverse the catch-all settings, as you've indicated. Then assuming you've got everything setup as far as DNS/MX records and whatnot the zimbra.domain.com server should start handling all email for domain.com
Also, to confirm, if zimbra is the primary server now, does it mean emails coming to my email account @mail.account.com will be delivered to mail.account.com. As it is now, mail.account.com is on zimbra.mail.account.com.