You may see programming serial flash with a Serial Vector File (SVF) converted from JIC file (for Active Serial mode) fail when using JTAG Chain Debugger in Intel® Quartus® Prime Software. This happens on both Micron* and Macronix* flash devices.
This failure is known to occur if the TCK frequency of hardware programming cable (e.g. Intel® FPGA Download Cable II) is different to the TCK frequency set during SVF generation (when converting JIC file to SVF file).
When converting to SVF file, set the TCK frequency to be the same as the hardware programming cable.
It is recommended to set the TCK frequency to 6 MHz for both.