The driver software communicating with the Hard IP core must be aware that a configuration read of the Vendor ID register was pending and that the Completion without data and UR indicate device/bus/function not present. If this request was from higher layer software the driver should report a Vendor ID=0xFFFFFFFF to meet the expectations of system software components.
The Altera® Hard IP for PCI® Express is a root port device, it is the surrounding Root Complex that is responsible for reporting the 0xFFFFFFFF Vendor ID.