It enables offline support for all games by default, which I feel is a useful feature.
To make sure it updates isn't that complicated. There are two ways:
1) change the timestamp at the top offline.appcache file. Alternatively just export again, the new offline.appcache file will have a new timestamp. This file needs to change for the browser to notice there's an update.
2) browse to the game again. Check the browser console (Ctrl+Shift+J in Chrome) and you'll notice it's downloading the update. When it says the update is ready, hit refresh and the update loads.
Mobile browsers are harder since you can't see when the update is ready. You can use the Browser object to check if an update is downloading or when it's ready and display this in-game.
Just upload to a different URL or rename the folder it's in. The browser will treat it as entirely new.