I had assumed that you if you use a cache manifest and then refresh the manifest, that the browser would request all of the files again. However, I have found that I needed to explicitly set headers in all of the files in the manifest to tell the browser not to cache the files. I believe that once the manifest tells the browser to request the file again, the browser treats it like any other non-manifest cached file. Maybe this is an error with Chrome, but I feel like I saw this in another WebKit browser.
Regardless, set the headers for the files in the manifest to never be cached and they should reload when you update the manifest. If these files are used outside of a manifest page, you may need to actually cache the files depending on your needs.