Thanks for the idea submission. This is something we've heard from a few customers and would like to implement. At this point its a matter of getting it prioritized with other work. Please continue commenting and staring this post so we can get a sense of how many people this would impact.
This would be a great right-click action in the warning box - so when you see "missing fields" you could right click in the warning box and say "forget this one" or "Forget all missing fields in workflow".
Currently getting an error where I deleted a field from a Layout tool and am unable to forget missing fields so now I have to delete the layout tool and re-insert. Clearing all missing fields would be great.