Hi,
You mentioned that data pin is 1 when nCSO is 1 and data pin is 0 when nCSO is 0, are you saying AS_DATA1 pin as shown in user guide below:
https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/hb/arria-10/a10_handbook.pdf
if it so, then the problem might be due to the flash device itself or the bitstream. Because the data should be sending in appropriate format instead of HIGH all the time or LOW all the time.
May i know have you tried to program JIC using our Quartus? This is to check if the bitstream generated is correct or not.
Also, i would like to check, during the generation of RPD file. Have you selected the correct information? such as the correct flash device & also the configuration scheme which is Active Serial x1
May i know have you followed this guideline as shown below when using generic serial flash IP?
https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/ug/ug-gen-sfi.pdf
You mentioned about taking control of JTAG chain by causing an error to it. Apologize that i dont understand about this. Are you saying that you want to access flash memory using JTAG such as using USB blaster II?
Regards,
Aiman