The Board Update Portal allows you to write new software image to user software portion of flash memory.
From the Start Menu select All Programs, Altera, Nios II EDS, and then Nios II Command Shell
elf2flash --base=0x24000000 --end=0x27FFFFFF --reset=0x24430000
--input=yourfile_sw.elf --output=ext_flash.flash
--boot=$SOPC_KIT_NIOS2/components/altera_nios2/boot_loader_cfi.srec/strong>
Browse to the hardware file and the software file (if required), respectively.
Click Upload, and then wait for the files to be written to flash. Progress is displayed from 0 to 100%.
Ps: Please make sure user FPGA build has already been programmed into DUAL COMPRESSED IMAGE #1 section before it boots up from user software image.