“Backward compatible with PCIe Gen3 x2, PCIe Gen3 x1, PCIe Gen2 x4, PCIe Gen2 x2, and PCIe Gen2 x1”
I do not think that is the problem if it is a WD_BLACK SN750 NVMe SSD (WDS500G3X0C) or a WD_BLACK SN850 NVMe SSD (WDS500G1X0E-00AFY0).
Since it is not being seen at all my guess is that there is a power issue. The only number I can find for peak power (10 microseconds) is for the sn750 (and sn850 NVMe) of 2.8 A, which at 3.3 volts which would be 9.24 watts.
If there is sufficient power for the VF2 and the peak power of the NVMe then the other option would be that the edge connector is not making full contact. I’d remove and inspect both with a bright light under high magnification, using normal antistatic procedures.