NIOS II and Cyclone III Remote Update

Remote update core is something related to FPGA hardware and it doesn't know anything about Nios or whatever is implemented inside FPGA.

You could have implemented another processor instead of Nios, and this would have a different bootloading method: then, the uP bootloader is only a matter of the specific FPGA configuration and remote update core has no effect on it.

In the case of the epcs controller for Nios system, the Nios bootloader is embedded in the controller core itself: this means the bootloader is encapsulated in epcs controller hw logic (sort of PROM bits) when the core is generated and fitted into the fpga image.

That's why you need to assign the firmware position before generating the fpga image and you can't change it by simply modifying the remote update settings.

Please let me know if you got it clearly or if you need futher explanation.