Dear c.johnson@lightstat.com,
As far as I know there's no restriction for write the EEExxx registers, after the Program Partition command this register should be changed but the use of this command needs to have the following consideration that is found in the reference manual (32.4.12.15 Program Partition command):
The Program Partition command prepares the FlexNVM block for use as data flash, EEPROM backup, or a combination of both and initializes the FlexRAM. The Program Partition command must not be launched from flash memory, since flash memory resources are not accessible during Program Partition command execution.
The size should be read back using the Read Resource command .
Also, could you share how are you building the command?
Best Regards,
Alexis Andalon