How to reset the ALTERA Cyclone II after loss communication during firmware upgrade?

With the attached external EPCS4 device on a Cyclone II, you can use the USB blaster to download the .sof; the SRAM based program image that resides INSIDE the Cyclone II. The external EPCS4 can be absent or blank when you do this.

If your Cyclone II image is correct, it should then have the Altera serial flash loader module in your design. For example, my CycloneII board with an attached EPCS4 device has this in its program image:

   // Altera Serial Flash Loader module

    // Allows external JTAG access to the serial config eeprom for programming

    sfl	sfl
	( .asdo_in		(1'b0),		// not used
	  .dclk_in		(1'b0),		// not used
	  .ncso_in		(1'b0),		// not used
	  .noe_in		(1'b0),		// always enabled
	  .asmi_access_granted	(1'b1),		// external JTAG access always
	  .asmi_access_request	(),		// not used
	  .data0_out		()		// not used
	  );

So if the Cyclone II is unprogrammed, ONLY the Cyclone II device will show up in the JTAG chain using Quartus programmer.

Once you download a .sof image to the Cyclone II that has the above code in it, the JTAG chain will now also show the EPCS4 (virtual) JTAG device.

And then you can program the EPCS4 device with a new image, reset the board, and it should boot from the EPCS4 (assuming you have the correct serial boot mode setup selected).