From what I read from those links you posted was music being deleted from the apple devices them self (iPod) when music was put on them through other software or that was using a hacked version of apple's DRM. I actually remember that Real Networks had figured out a way to put a hacked version of apple's DRM on music purchased from them in order to keep their music protected while still being compatible with apple's devices. Apple was able to detect this. But from what I recall and what those links say, it did not hut through the computer and delete them. It would remove them from the device or inform the user of the music with invalid DRM and ask them to restore the device.
I have never seen or heard of iTunes simply deleting MP3s or any other audio (or even video) format for simply not having been ripped by it.
