How do I reload changed files only using offline.appcache?

Is there a way to make sure the offline.appcache updates changed files only, instead of all files? Normally offline.appcache will ignore unchanged files by default, but it's not working like that now. I'm using the latest version of Chrome.

It should do that already, providing the server caching is set up correctly. If the offline cache requests a file again, it can still use the existing browser cache.

So will the browser recache everything when it found one of the files is returned 404 error?

No, it would simply cache that the file returned 404 not found. But that should not ever happen unless you didn't upload the whole project.

I just found that when the game is hosted on dropbox, the cache manifest will work just fine (retrieve modified files only). But then when I tested it on github pages, the browser will simply redownload all files even only a single file is modified. Is it related to cache headers that set by github pages?

Yes.