Note sure if I agree with the latter part. With the new SWUs being similar colors as last year's SSWUs, I've caught myself more than once reaching for the wrong piece of paper when heading off to the airport in a rush.

Once, at FRA, I accidentally handed an SWU to the check-in agent where a SSWU was required. She kindly pointed out the need for a different type of certificate. This, in my opinion, was the only appropriate way to handle the situation. Same thing if you confirm an upgrade prior and then show up without any certs at the airport: The agent should inform you that you can not get the upgrade. Period. Notes on the file, IMO, could lead to lots of misunderstandings...