That is an AS+JTAG configuration scheme.
Can you detect the FPGA? If so, your JTAG chain should be OK.
It's normal that you can't detect the EPCS4 device via JTAG, as it doesn't even support JTAG.
EPCS can be accessed over JTAG using the Serial Flash Loader, but it doesn't show up in the JTAG chain.
Basically, the FPGA is first programmed with a firmware that include the SFL and then the EPCS is written through the FPGA, like this:
Quartus --> USB --> Byte Blaster --> JTAG --> FPGA --> AS --> EPCS4
To do this, you need to convert your .sof into a .JIC. Check AN370 for more details.