Do you see the said com port in the Windows Device Manager? If you see it there, it should also be appearing in the GCS, but if not it's probably a driver issue maybe even hardware issue.
I'm not exactly sure what you're trying to do, as I understand you're trying to reconfigure the FC by connecting it trough USB and then selecting a "Serial: COMX" option in the GCS.
Why don't you try to select "USB: CC3D" (or something similar) option which is the default to use when configuring the board?