Error while trying to program EPCS flash in indirect SFL mode

Is the EPCS device an Altera branded device or from a third party vendor? You may be seeing that error because the FLASH programmer doesn't recognise the ID of the configuration device fitted. There are plenty of vendors manufacturing serial FLASH parts but unless Quartus recognises the device ID it won't program it.

The way around this is to use the Nios FLASH programmer available from within Eclipse - having programmed your FPGA with a design containing a Nios core. You can set up the Nios FLASH programmer to work with third party devices successfully.

Is this you're own hardware? Have you ever had the FLASH device working? Is there a build fault?

Regards,

Alex