Once finished, press the blue “Apply & Close” button. If you get a message about “Duplicate files” you have to review the files listing for duplicates. In fact some times W3 Total Cache does proposes lists with redundant names but it will only accept unique names when you want to submit your changes.
The large popup window will close. The underlying Minify window now has its “JS” and “CSS” sections filled. Press one of the blue “Save all settings” blue buttons.
W3 Total Cache will now show: “To rebuild the minify cache use the [empty cache] operation. Get minify hints…” at the top of the screen. Press the [empty cache] button or go ahead and completely purge all caches (menu at the top of the screen, under “Performance”). If you have done your work well, you’ll see come to life most if not all of the previously broken plug ins. Congratulations, you are done!