Ashley I've just spelt if wrong, did not changed the filename after export. I think I do exactly what you described.
1. New export from C2.
2. Uploaded all of the files zipped as a hosted app to CWS.
3. Went to new tab in Chrome, started the installed CWS application, used it for several minutes to take enough time the update to complete.
Espected: the apps updated in the background, and the new music file is loading from the cache.
But I get: the old music file is playing from the Chrome's cache (saw it in Chrome's Dev tool/Network).
Additionally I see the new version number (1.0.1) of my app in the Chrome/Settings/Extensions list.
Things that may cause the problem:
1. I used to remove the music file in C2 and than added it with the same filename. The source file was story1page1.wav and the encoded story1page1.ogg. The old and the new file is not the same in size.
2. I noticed, that C2 places this updated music file at the bottom of the offline.appcache file.
3. Probably some bug in Chrome Webstore itself with publishing/distributing updated versions of offline.appcache file (I searched for similar threads in Chrome Webstore Dev discussion group today with no success).
4. Probably some bug in Chrome Web Browser (I use 20.0.1132.57m). I found a bug that seems to be similar, but with V18 of Chrome: code.google.com/p/chromium/issues/detail