Programming the .aocx file with PCIe instead of JTAG cable

You do not need any additional drivers to program the FPGA via JTAG. However, to program it via PCI-E, you must have correctly set up your board and installed the PCI-E driver provided by the BSP and programmed your FPGA with a base OpenCL design to enable the PCI-E core on the FPGA.

If your JTAG cable is connected but quartus_pgm doesn't find it, try killing "jtagd" and then running "quartus_pgm -a" as root. In my experience, it is important that after every machine reboot, quartus_pgm is first run as root or else the cable will never be detected. After that, the cable will be detected by quartus_pgm regardless of which user is invoking it. In the next step, since it seems your PCI-E core on the FPGA is broken, you probably have to reprogram the FPGA via jtag with an OpenCL design and then reboot your machine. After that, PCI-E-based programming should work.