Hello Terry,
You are correct that the flash programmer is only dealing with one of the flash chips. The SODIMM module was created long before the Nios II and flash programmer and doesn't really fit well with it's view of flash memory. We unfortunately don't yet have a solution for writing a filesystem that is larger than 2M. If you were able to somehow split the flash file at the appropriate place, you might be able to download the two pieces independently to each chip using the command line nios_flash_programmer.
Dennis Scott
Microtronix Datacom Ltd.