Hi - I'm sure Patrick didn't mean to give you that impression. Qdabra supports this forum, and if we have a product that may help you, we suggest it - but that isn't the main goal here.
At any rate, you could certainly create some kind of a script to do this yourself. If you open the XML file in a text editor, you'll see the location of the old template in the first line - after "href". You can change that to the location of the newly published template. Obviously, this can be done by hand, but you mentioned thousands of files - I think an automated method would be the way to go.