As no rulers have updated their banners so far, it might be better for the dev team to manually update the flags where nothing but transparency has changed.
By far the easiest way for that to happen is for you to simply take the updated files and put them in the directory, then either update the DB yourself or let me know so I can do it. (Assuming that all the filenames are the same, just with .jpg or .gif replaced with .png.)
...Also, it would be convenient if you could dump a fresh copy of the /icons/ directory on the dev server once you've done so; it's getting kind of behind on the banners again