NIOS II and Cyclone III Remote Update

Kosh is right, you need to change the bootloader, because the default one assumes Nios firmware is located just after fpga configuration data starting at address 0; then you load new fpga configuration, but the old nios firmware.

You need to replace the epcs_controller_boot_rom.hex file in Quartus directory with the customized bootloader image and then rebuild the fpga project.

Pay attention that sopc builder overwrites this file with the default bootloader whenever you regenerate the sopc system! Then you must backup your custom hex image and replace it every time you rebuild sopc.

What kosh suggested is indeed the standard solution for generating a remote update firmware image.

AFAIK there's no way to automate the procedure and make it easier.

Anyway it is not that difficult. Consider that the primary fimware (usually referred to as factory firmware image) is seldom changed, so the fixed address location for the updated firmware is not a great problem: normally you only need to generate the special bootloader once.