The banner is linked to the template being used so whenever a page uses an out-of-date template, it will appear. I understand that this might seem trivial, in the long-run the use of out-of-date templates can cause problems for organisation and administration of the Wiki. The purpose of the template is to bring this to the attention of contributors.
In many cases, the replacements templates use the same fields as the older versions so it might just be the case that you have to change the name of the infobox. Once again, I know that in some cases it can be a time-consuming task to change over but it means that the pages are more robust moving forward.
If you still have concerns, feel free to send me links to the pages in question on here, or on the forum (my username is "jamescfm") and I will offer advice and help you out with editing where I can.