Problem with flash programmer

Why did you uncheck 'Program software project into flash memory'? Is there no Nios II program you want to load? If so, you could use the Quartus Programmer instead of the Flash programmer.

For only loading a .sof file to the flash, you can go to File-> Convert Programming Files..-> choose e.g. .jic File as programming file type -> choose the right flash device -> click on Flash Loader and choose your FPGA type -> click on SOF Data and choose your .sof-file -> generate. Then in the Quartus Programmer you can choose that .jic File and start programming the Quartus. Every reset of your board the configuration will be loaded from the flash into your FPGA, because you added a Flash Loader.

BTW, I got that 'There are no Nios II processors available which match the values specified. Please check that your PLD is correctly configured, downloading a new SOF

file if necessary.' message for several reasons already. Once I had some wrong clk assignements in the SOPC Builder, or in the Assignement Editor, or one of my user components have not been programmed well yet. In all that cases I got that message, just because the FPGA configuration was 'bad'. And sometimes it helped just to shut down the Nios IDE and the Quartus, or sometimes it was enough to only close and reopen the Quartus Programmer or once it helped to restart the PC. But the real reason for that message was one of the errors descriped before, what turned out later. Same happened to a colleage. Just to be complete about that error message.