New Contributor
New Contributoredit: got the factory build fixed, sorry for false alarm.
I regenerated the .sof with Active Serial x4 specified so that when converted to .rpd, the Configuration Mode would be consistent. I also programmed the FPGA directly with this newly-generated .sof to ensure it works correctly, and it does.
Note that I do need to revert the MSEL pins to the default of "10" to specify AVST x16 for the factory build to program... I forgot to switch it back and thought I had bricked the board when the factory build wouldn't request an IP address via DHCP for me to connect to the Update Portal. Switching the MSEL pins back to default makes the factory build work again.
So, the original .sof was generated in Quartus with Active Serial x4 specified in the Quartus > Assignments > Device > Device and pin options > Configuration menu, and then the .rpd was produced using File > Programming File Generator selecting Active Serial x4 as the Configuration Mode, .rpd as the output file type, and the .sof generated previously as the input file.
I converted that .rpd to .flash using the exact nios2-elf-objcopy command you indicated earlier (however, run from within a Windows command shell and not the Nios2 command shell). This .flash was then uploaded through the Board Update Portal, and after successfully completing I powered off the board. With power off, I switch the MSEL selection back to "01" to indicate QSPI x4 normal mode, and SW3.3 to load User Hardware1.
Powering on the board, I get four red LEDs blinking once per second and the design does not function. This happens with both "01" and "00" MSEL setting. If I revert back to "10" (AVST x16), it waits a few seconds then shows a single red LED solid on. Switching SW3.3 back to factory build, the Board Update Portal design successfully configures.
