The quickest fix for me is to exit and restart LR. I've been having this problem when using the 'Right-Click' Edit in feature for both NIK and on1 modules.
If I access the on1 plug-ins via the File->Plug-in Extras.. method the flicker does not happen. Unfortunately there is no way to use that method with NIK.
My current workflow is to use the File->Plug-in Extras... for on1.
When using a NIK plug-in I immediately exit and restart LR after returning from the NIK module. A pain but it does work for me.
BTW, this 'flicker' after using the Edit-in feature has been happening for me since LR2.
Many people have reported this problem, which Adobe has acknowledged as a bug. See this thread in the official Adobe feedback forum for workarounds: LightRoom 6 TIFF file reloads after each Develop edit, potential data loss. Be sure to add your vote and opinion to make it more likely Adobe will prioritize a fix.
Thank you very much.