You shouldn't lose your settings, but if you want to be safe, you can use a SysEx librarian program on your PC or Mac to back up the settings. If the settings get wiped during the upgrade, you can send them back to the Mastermind.
To back up:
Connect the Mastermind MIDI Out to the PC's MIDI in.
Set your SysEx librarian program to receive.
Enter setup mode on the Mastermind (Hold 1 and press 3)
Press the Function button until the display says "SEnd"
Press the bank up button
The Mastermind will send its configuration to the PC. You can now save the file.
To restore:
Connect the Mastermind's Remote In to the PC's MIDI Output
Power up the Mastermind. Make sure it's in normal operating mode
Load your saved settings in the SysEx librarian program
Make the program send the data
The Mastermind should flash a couple of times, then reset
Your settings are restored!