I have implemented remote update on cyclone IV FPGA board. After the power cycle the factory image is configured and then the nios boots correctly. When I configure the application image without the application hex file, the sof is configured properly. I checked it by using PIO in Qsys and assigning different values to the fpga pins. In the factory configuration the fpga pin has 3 volts and in the application image it has 0 volts. I was also able to download elf file on the application image from eclipse.
Can you try double confirming and ensure that you have a valid .mif or .hex to process. Recheck and specify the location, including the file name and extension as well and try to reboot.