Cyclone IV and Nios II Firmware Update

No the Nios2 programmer just flashes the contents it reads from the given .flash file, it doesn't write anything else. My guess about the +15kB is that it zero fills the last flash page, but I can't be sure.

There are two things I see in your set of commands: first when you write this:

cat SoftwareFirmware.bin HardwareFirmware.bin > Firmware.bin

the software will be put in the flash before the hardware, and the FPGA will not boot. You need to put your two binary files in the other order. Second I'm not sure about the use of nios2-elf-objcopy to translate a srec file to binary. I've never used it that way and I don't know if it gives the expected results... Maybe you could try to use another tool (such as the very good srec_cat (http://srecord.sourceforge.net/)) to generate the binary file. srec_cat can also to the concatenation of the two .flash files, using the addresses to place the data correctly, so you are sure they it will always be put in the right order in your resulting binary file.