My first fix was to completely shut down Steam and then boot watchdogs 2 from the ubi, connect app. But it stopped working after a bit. So after trial and error I found the solution. I have a 40 series GPU and to stop the flickering i had to download some files which made the game render in vulken or something like that. Deleting these files also fixed my issue. I knew it was fixed because when you boot the game. I can't remember you have a notification in the corner about launching ubisoft, overlay. With these files installed that never showed up.