You should unplug all the x1 riser connectors except for the one in the primary x16 slot before upgrading. I just use the Microsoft media creation tool to create a bootable flash drive with the latest build and always nuke the system drive to do a clean install. The media creation tool automatically creats a bootable flash drive with the latest Windows 10 build and updates.
https://support.microsoft.com/en-us/help/15088/windows-create-installation-mediahttps://www.techspot.com/downloads/6734-windows-10-installation-tool.htmlMake sure to boot off of the USB flash drive UEFI partion from the boot menu for the Windows installation. After Windows installs I run DDU in safe mode to remove the existing driver and set Windows to not automatically install drivers. Then I shutdown, connect all the risers back in the PCI-E slots and install the latest driver. I also set a group policy to disable driver updates from Windows Updates.
In the Windows 10 Pro Group Policy Editor you can keep Windows Update from updating the the drivers.
gpedit ==> Computer Configuration ==> Administrative Templates ==> Windows Components ==> Windows Update and set 'Do not include drivers with Windows Update' to enabled.