11.7. BIOS Enumeration Issues
Both FPGA programming (configuration) and the initialization of a PCIe link require time. Potentially, an Intel FPGA including a Hard IP block for PCI Express may not be ready when the OS/BIOS begins enumeration of the device tree. If the FPGA is not fully programmed when the OS/BIOS begins enumeration, the OS does not include the Hard IP for PCI Express in its device map.
To eliminate this issue, you can perform a soft reset of the system to retain the FPGA programming while forcing the OS/BIOS to repeat enumeration.