I have a similar problem with a Jetson board. If I turn off the power long enough (one night) and then turn it on, the only PCI card is not recognized and I have to power-cycle it to get it running.
My startup logic now power-cycles it until the PCI board is recognized; it works, but it's not a great solution.
echo 1 > /sys/bus/pci/rescan
sleep 1
Sometimes it brings the PCI card back, so I just run this as part of my boot sequence.