JTAG chain not seen unless factory_load switch is set

I went to the Update Portal and re flashed the HW FLASH image the current FLASH contents may be configuring the FPGA and running NIOS II SW causing some

weird JTAG "side effect" where the JTAG chain was no longer intact.

Once I did this , the application came FPGA application came up running from power up, the JTAG chain check from the tools drop-down menu worked and I was able to program the same FPGA code via the tools programmer.

Thanks for your help ... I still need to get the FLASH programmed with NIOS II SW + boot loader and have the FLASH read interface in the FPGA that I copied from the BTS example.

Thanks for all your help. Bob.