I have this screen flickering as well. 
Very bad bug, when it happens restart of the software necessary.
!! Dangerous for people with epilepsy !!
Exact steps how the flickering happens:
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First Flight after MSFS start everything perfect.
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Pressing ESC after Flight to bring up the In Flight Menu starts the Flicker. (Every time in my case)
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Going back to main menu everything is fine
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Starting a new flight flicker is back - this time all screen flicker, not only top half:
Restarting the software is the only way to get rid of the flicker.
Edit: Turning weather to clear skies fixes the issue.