The fastest way to swap everything would be to shut down both servers, swap their database files, and start them again.
Typically stored under at "C:\ProgramData\JH Software\Simple DNS Plus\sdnsplus.db"
Alternatively, if you want to make all secondary zones on one server into primary zones, and all primary zones on the other server into secondary zones:
To promote all secondary zones to primary zones on your current secondary server / future primary server, you can use the "Bulk update wizard".
Click the "DNS Records" button, then in the "DNS Records" window click the "Bulk..." button in the toolbar, select "Promote secondary zones to primary zones", and follow the prompts.
As for the current primary server / future secondary server - the easiest way to get this set up correctly is actually to delete all the zones, then set up Super Master/Slave (Options dialog / DNS / Local zones / Super Master/Slave).
This needs to be configured on both servers so that they can synchronize the zones automatically.
Of course, before you do any of this, make sure to back up everything first - see https://simpledns.plus/kb/50