I had root and I just updated my phone to 4.4 I updated my phone to 4.4 while it was rooted, and now in my setting its says its 4.4 and when I wanted to download pokemon go it said ''Your device isn't compatible with this version''
Updating from the stock vendor while in root will unroot the device as the new image downloaded is not rooted. Many devices are not compatible with many games.

 Can you be more specific ! Which device you're using and what ROM you're using ?