I assume that you are working in Dreamweaver. If you have a website based on the template displayed in the Files panel in Dreamweaver, go to: Edit> Templates> Export without layout ...
You will be asked where you want to save your files. If you plan to do this only once, uncheck the two boxes in the user interface. If you need to do this several times, look at the help files that they can tell you when you may or may not want to select these options.
If you want to stop working with the "old" file and continue to work with files in Dreamweaver, I would export the files without markup to another folder, then change the site definition to point to a new location, or perhaps replace the contents of folders with Dreamweaver closed ( so that he doesn’t want to look through everything, to try to find updated links)
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