Preserving sectors in an EPCS

Yes it does sound convoluted. However, consider the following:

1 - Your scheme is no more convoluted than using the Quartus programmer with the JIC method. The programmer downloads a special image to the FPGA which it can then use to communicate with to reprogram the flash. You'd basically be doing the same thing.

2 - You don't have to use AS for the initial config. You could program your special image into the FPGA and use the nios2-flash-programmer for your initial config. No reason to maintain two processes.

3 - I suspect your proposed method still yields a faster programming time with the NIOS over the AS method.

Jake