You can performed it using TCL file where you are able to modify it and re-run the compilation.
You may refer to https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/manual/tclscriptrefmnl.pdf for the full supported TCL script supported in Quartus
Below is the step to performed it in TCL file.
- project_open -current_revision project_xxxxx
- set_global_assignment -name STRATIX_JTAG_USER_CODE FFFFFFFF
thanks for your reply. I guess that will effectively update the qsf file? I had figured out a way to do the same by nobbling the code directly in the qsf but reasoned to myself that as the gui is presumably calling quartus_asm under the hood that it must have been passing it in as a parameter.