It is obvious that the computer hardware capabilities did not change. Some driver or update that you installed has changed the way the operating system is reporting it. We cannot know what that may have been. You will need to investigate through the Windows 10 updates to find the culprit. Perhaps rollback a driver to a previous one, etc.
I've dell 7566 gaming I5-6300HQ+GTX960M and use M.2 Nvme WD Black 256GB with Windows 10 with lasted update, and update driver to. So i've check my system at CPUZ and GPUZ, But GPUZ at PCI Exprees mode just show PCI-EXPRESS X16 3.0[NAME] 3.0  For First time i use (about 3 month ago) it just x16 @ x16 but to day it go wrongs  What happen about my Laptop, anyone who can explain me about this issue ?  and How can i fix it please guide me. PS.   - i don't worry about FPS but I want to Know about Sources to make it happen and find out how to clear it for future - Sorry For My English Language, And Greeting From Thailand  With Sincerity 
About PCI EXpress @ GPUZ