You could do that, just dont change the file-header part of the file, only the file data. Then you would get a very weird sounding file 
that could actually work ! If you had already spoken with the person and you told him what part of the file data you are gonna change and with what(kinda like a public/private key), then you could build like a small arduino crypter/decrypter based on your previous deal made with the other person and somehow connect it to the walkie talkie. I don't know if it is possible but the idea of changing the file data of a sound file and sharing it with someone else who knows how it's been modified could work.
