Trouble Of Board Description Editor

If you just want to program the flash you don't have to make a board description. You can run the command line tools quartus_pgm, sof2flash, elf2flash and nios2-flash-programmer manually to program the flash. You convert the elf file with elf2flash then you program the sof with quartus_pgm into the fpga and finally run nios2-flash-programmer to program the flash files.

And if you make a board description you don't need to specify a netlist file. I think the process to program the flash is not well documented. The documentation implies that in order to use the flash programmer you must have a board description, and then it does not detail what steps are really necessary and what is not needed when making the board description for just programming the flash.