The Board Update Portal allows you to write new designs to the user hardware 1 and user software portion of flash memory.
From the Start Menu, open Nios II Command Shell
sh build_hw.sh yourfile_hw.sof 1
elf2flash --base=0x0 --end=0x0FFFFFFF --reset=0x06700000
--input=yourfile_sw.elf --output=yourfile_sw.flash
--boot=$SOPC_KIT_NIOS2/components/altera_nios2/boot_loader_cfi.srec;
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%.