I have an RX Vega 64 Liquid in Primary PCIe port and
R9 Fury X in secondary PCIe port on one of my Asus Z 97 motherboards with a i7-4790K CPU.
I downloaded and installed AMD Adrenalin 18.11.2 and ran clean install after DDU uninstall in safe mode and no internet connection.
There is no way the Primary PCIe slot can run in x16 with a secondary GPU connected on that motherboard.
This is the first time I have seen that reported incorrectly.
Bios reports both PCIe slots running at PCI 3.0x8.
It looks like a bug somewhere in the Driver. ... unless I am missing something about the RX Vega 64 that I do not understand.