I made an encrypter/decrypter a while back. It supported any size of project, as well as changing the default DEADCAFE key for the encryption to make it harder for someone to break. As far as I know, all the tools out there that can break an unpack an archive easily without the user needing to know a thing require the user to know the encryption key.
I will see if I can dig it out and post it up.
EDIT:
That reminds me. Has anyone actually tried to encrypt the audio using the default encryption method and see if it still works?