You are still misunderstanding the suggestions in the other thread.
https://www.edaboard.com/threads/322369/
They have been talking about a way to program the serial flash through JTAG. A working JTAG connection to the FPGA is required for indirect JTAG programming as well as debugging.
You have reported that the "JTAG header" is connected to the EPCS device. It can't be connected to the FPGA JTAG pins at the same time and isn't suitable for debugging. That's the whole story.