After a long time using an old version of WiinUSoft, that required the toshiba stack, I finally decided to upgrade the software in order to use the Switch Pro Controller as well. Knowing that the Toshiba stack was no longer required I uninstalled it, reinstalling the default bluetooth drivers afterwards.
So, using WiinUPro 0.9.2: - I was able to sync the Switch pro controller, and connect it like normal. - I was able to sync the WiiU pro controller, but as I connect it, the screen shows nothing.
I will add images to show what appears on the screen
If Windows Bluetooth still has a reference to the controller the sync button method will always fail. You'll have to remove it from Windows first. WiinUPro won't work with it connected just generically, it has to either be connected through the Toshiba Bluetooth Stack or using the sync button.