Yes, head banners could be a little bit different for some of the templates, so in this case to save updated templates (it is suggested to have updated templates) and to have old head banners I can suggest you copy head banners images from user's sites (where it is necessary) and let users upload this pictures into their sites.
I do not think that there should be a lot of customers with such situation. Am I wrong here? Just give cutomtomers instructions to copy necessary head image from published site, in Wizard upload this banner and select it for site one more time.
Hope it helps.