Deleting the .ogg files is *not* a solution. You should definitely not do that. You will stop audio playing on other platforms instead. What I think is actually happening is this:
1) you upload your game and run it, but the server is set up wrong
2) the browser caches broken versions of the .m4a files and doesn't play audio
3) you fix the server
4) by changing offline.appcache, you make the browser re-download the .m4a files which work. It is not important what change is made, just the fact you changed it makes the browser check for updated files and notice the fact you fixed your server.
Construct 2 changes the content of offline.appcache for you every time you export (the timestamp is at the top of the file). So re-exporting alone should be enough to fix it once you've fixed the server.
If in doubt try exporting to a new URL after fixing the server - it will use a completely new cache.
If you delete one set of sounds, it WILL break audio on different platforms, so don't do it!