Error: Erase failed at offset 0,

what FPGA are you using? If it can use a serial flash loader (SFL) design, then you could access the flash from the Quartus programmer without going through a NIOS system. That way you should be able to test the EPCS flash and know if the problem comes from the EPCS itself (or the connection between the EPCS and the FPGA) or from the NIOS/SOPC component.