Convert Programming Files tool and multiple Nios processors

Have a look at the "using the flash programmer from the command line" section in the nios ii flash programmer user guide (https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/ug/ug_nios2_flash_programmer.pdf). There's a section on "programming both hardware and software into an epcs/epcq device". Look through that. I think sof2flash, elf2flash & possibly bin2flash between them should solve your problem. These allow you to convert files and generate S-record files with offsets. You can then combine them and, if you wish, convert them to a .pof, or simply use the command line programmer.