I'm not quite sure I understand - but the Emulator stores the contents of 'storage' in the web browser's 'local storage'... So I guess if you used a different web browser (or an emulator hosted from github vs espruino.com you would have different storage contents)
Also, you might have just been uploading to 'RAM' when you tested? In which case it won't overwrite the old one...
I noticed that some times an app (a clock/watch) executed by the emulator is not the same that I uploaded to storage and tested on a previous time but an older one.
Curiously when i upload a new file to storage during all the session it really seems properly overwritten. For example I can leave the app and execute again from launcher or storage and always it is executing the updated code.
Have you experience it? Ideas besides clearing the cache/storage?