Similar to the setting that you have in many individual tools (join, append, select, et al) where you can go to options and choose to "forget missing fields" it would be nice where you could go to options for the entire flow and "forget missing fields".
This would remove the headache that you have with large flows where you make a change(s) then have to go back through each and every tool to "forget" within that tool. Yes you could still do it individually, but if you chose, you could also do it universally for the entire flow all at once to all the 'missing fields'.