PCIe device disconnect/disable needed to reprogram FPGA

I am using the Altera Stratix IV dev kit. The FPGA is in a PCIe slot on a system running Linux. Is there a way (i.e., some Linux commands or some other method) for me to be able to disconnect/disable the PCI device from the bus so that I can load a new .sof onto the FPGA, than reconnect/reenable the device after the FPGA has been reprogrammed? I need to find a way to reprogram the FPGA without causing the Linux kernel to panic due to PCI slot issues caused when the FPGA is reprogrammed.

For the purpose of this thread, please assume that loading a .sof onto the FPGA is the only way that I can program the FPGA. Also, please assume that I do not have the luxury of re-booting the machine. As a result of these constraints, I am ensuring that my PCIe BARs and config space do not change from .sof to .sof.

I am considering coming out of retirement and resuming my other career if I can't get this to work. :D