Writing the .flash file to flash on the target

Altera .flash files only use S0, S3 records and from Quartus 10.1 also S7 records on the Nios code file. (at least when using EPCS, which I have experience with)

You can just skip the S0 records, decode the S3 records and use the S7 records to find the end of the file.

First you have to erase the area of the flash you are going to write two.

Then decode the S3 lines until one flash block of data is buffered to a RAM and then write the whole block the flash.

You have two flash files, one for the FPGA configuration and one for the Nios code. These can be concatenated.