why dont you just get the *swf file, or whateva kind of format the banner is in,
open up flash 8 > import to stage > click swf file> and then create a new layer (this will be your layer you put in your own websites url, and then paste it over the other one (as long as your editing layer is on top of the original source, it will be pasted over (similiar to photoshop) )
hope that helps.