Mine does the exactly the same thing. Only with the Netflix application, not with Netflix via a web browser, or with any other program or video player I have tried. As a workaround, I can usually fix it if I pause the flickering movie and then cycle the screen brightness from 50% to 75% to 100% to 0% to 25% and back to (my normal) 50%. It will play just fine after that, even in fullscreen, without any of the flickering. I use the Lenovo supplied battery/screen icon in the System Tray; it's five clicks and takes less time than typing this in. 
The Netflix App flicker is a horrible brutal flickering, btw, taking the screen from at least 100% to completely off and then back...
I'm gussing that the Netflix application is sending some commands to the screen that aren't supported on our OLED X1 Yogas. But that's just a guess; I'm not a Windows programmer. I suspect there are different ways to talk to the screen, and some of them override the (minimal) color management functions. Maybe the Netflix application is sending a command to set the screen to maximum brightness and there's something about it that our screen driver doesn't like.
For example, when I use Grover Podcast to view a video podcast, it switches my Color Setting from my normal setting (Photo Pro) to Native. But it's a nice citizen, switching to Native only while Grover Podcast is on top. I suspect that color mangement under Windows is not quite there yet and Lenovo is trying to build some (color management) into our OLED Yogas. Note that every time the Intel HD Graphics driver is updated, one has to manually re-install Lenovo ChromaTune (by forcing a re-install of the Lenovo System Interface Foundation) before Color Settings will work.
I wonder if the Netflix application has this problem on every X1 Yoga Gen2? If so, since it came pre-installed, I'm surprised that Lenovo hasn't done something about it.
Hmm, I just noticed you never mentioned what type of screen your Yogas had, I just presumed. 
Are they OLED?
