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It just sounds like you have a Nios whose only purpose is to reprogram the EPCS; not a typical application[/b]
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This is exactly what we are doing. With the Nios 2 you can program flash and EPCS devices from the IDE. It does this by configuring the FPGA with a minimal design used just for flashing. Since the EPCS has dedicated pins they don't come out of the Nios so some optimization was occuring that prevented the flashing of EPCS devices.
More info on the new flashing came be found here:
nios ii flash programmer's user guide (
http://altera.com/literature/ug/ug_nios2_flash_programmer.pdf)