welcome to the brave new world. Files in Moodle 2.x are different, very different from Moodle 1.x.
In Moodle 2.x land, we are encouraged to disgard the notion of "Course files" containing files that may or may not be shared between activities.
Instead, each activity has it's own files area. If you want a HotPot JQuiz to use an audio file, you should add both the JQuiz files and the audio file into the "Source file" upload area for the HotPot.
If you want to use the same audio file in several HotPots, you have to upload it to each of the HotPots. If you change the audio file, you must upload it again to each HotPot in which it is used. If you also want to offer the audio file to the students as a resource, then you have to upload it again, separately, to the resource.
Similarly and thusly, if your HotPot uses several images or sound files, you have to upload them all to the "Source file" area for that HotPot.
In Moodle 2.3 you can supposedly "link" files to a single source file, and you can also supposedly keep your files in a folder on the server's hard disk and use that as a "repository". That should allow you keep a single source folder on your server's hard disk to which you can upload files, and then the latest versions of the files should appear in your HotPots and Moodle resources. Unfortunately, it doesn't work, at least it doesn't work as I expect it to. Somewhere along the way the files get cached, and so although you update the source files in the "repository" folder on the server's hard disk, Moodle will cheerfully offer up the out-of-date version of the file, apprently completely unaware that there is a new version of the file in the repository.
That is my experience anyway. YMMV.
I am still searching for way to do in Modole 2.x what we were able to do very easily in Moodle 1.9, namely to upload files to a place on the server from where they could be shared between several Moodle activities, and from where the latest version of a file was always available and was used as soon as it was updated. I haven't been able to do that yet in Moodle 2.x. If anyone finds a way, I would be very grateful if they could share their knowledge on this forum.