I'm far from being an expert but my take on this would be:
If the banners have already been made and they are set to point at a specific page on your site then I don't think it will record the affiliate code so no sales would be credited.
If it is only a .swf file you have then it may be difficult but not imposible to fix. As far as I
am aware, there are now programs which can decompile a .swf file so that you can make changes to it.
If you have a .fla file then anyone with Flash MX on their computer could sort it and i would recommend sending it to the network and asking that they do so.
I hope that's helpful.
With best wishes.
Steven
--
Virtual Cards UK
http://www.virtualcards.co.uk