It is possible to modify your primary domain in MDaemon, but when you do so, MDaemon will rename all users, aliases, lists and other goodies as well. Sometimes this isn’t desired, one such case is to make an existing secondary domain into a primary domain.
Shut down MDaemon, backup the entire MDaemonApp directory, then open the MDaemon.ini file and find the following key:
[Domain]
DomainName=primary.com
Change the DomainName key to be your ‘new’ primary domain, then restart MDaemon and you should be good to go.
Make sure that your IP bindings, and account pruning are set the way you want as these settings follow the domain, and so the secondary domain’s settings will become the system-wide defaults when it’s converted to a primary domain.
One other thing you might need to update, the mdaemon@ system account *should* change automatically, but if anything goes wrong, do not try to change this account manually, instead just remove it from userlist.dat yourself, MDaemon will recreate it when MDaemon next starts. If you corrupt this account, any number of things will break.
Also, you need to manually update aliases pointing to the mdaemon@ account.