Ref 25416 - "You must manually reduce applicable qualified research expenses deducted on Form 1120S by $xxxxx of research credit from Form 6765 Section B". I did. It's still a critical diagnostic warning. 

Warnings are just warnings.

Once you do what the warning tells you to do, it will still be there.

Once you do what the warning tells you to do, you may ignore the warning. 

If you wear a shirt & shoes, you may ignore the warning on the door about that issue.