I did do this for the other archives. For the flyers, after reading about the flyer rebuilding problems, just copying them over suddenly became the better way. I've done it before with little in the line of issues.
I should add that clrmamepro is designed for romsets, and indeed is by far the best way to maintain them with ever-changing sets, with archives that contain only the updated rom images, and with many sets at a time. With much simpler things like these it is sometimes simpler just to throw the updated files in the media archive and let cmpro scan and verify it. Just because it also has a rebuild function doesn't mean it must be used alongside the scanner. This may well be why Roman separated the two, giving people the choice how to use his program.
That said, it was not my intention to upset anyone in my use of the software. I do much appreciate you answering my request for missing flyers, and especially as quickly as you did it.