In order to get the Arria® II GX FPGA Development Kit to load the FPGA from the defined User Hardware 2 location at 0x00C6_0000, you will need to use a command line to generate a flash file:
sof2flash --input= my_file.sof --output=my_file.flash --offset=0xC60000 --pfl --optionbit=0x18008 --programmingmode=FPP
(The optionbit start address is different, the first 4 bytes for location 0, the second 4 bytes for location 1, the third 4 bytes for location 2, etc.)
The sof2flash command generates two flash files, one is my_file.flash, the other is my_file.map.file for the option bit. They all need to be programmed into the flash.
However, the .map.file generated for the hardware 2 location will have one problem. If you program it into flash, the version byte at the end of the option bit sector will be overwritten. As a workaround, read the version byte first and store it into a flash file (for example, a.flash) and then program the a.flash again to resume the right byte.
The two commands used to read a.flash and program a.flash should be:
nios2-flash-programmer --base=0x08000000 --read --read-bytes=0x018080 0x20 a.flash
nios2-flash-programmer --base=0x08000000 a.flash
Use the following programming sequence: