That’s a very old release, you might consider flashing something newer. However, this should not cause PCIe to fail.
A full serial console boot log would be best to see what PCI is doing during boot. For serial console, see:
During boot, if no PCIe is detected, then the PCIe bridge will be shut down and not show up from
lspci. No output at all from
lspci would be “normal” if there is nothing on the PCIe bus.
In the case of a failed bus, if signal quality of a faster generation device is insufficient, then PCIe will use a slower clock speed from a slower generation. If PCIe gets to the slowest generation (“gen. 1”), and there is still insufficient quality of signal, then the device will be removed and treated as if there is no device. Serial console boot logs should answer if this is the case.
Note that even if your system does not have a driver for the particular device that
lspci should still show the device as existing, and so there is indeed some sort of failure. Serial console logs would help answer what the reason might be.