Oh no it didn't! You need to send in a digital Sheppard to threaten the computer until it gives up the files. Then send in a digital Ronon to shoot it if it doesn't comply.

Is it possible that you'd somehow ended up saving it under another name or in another area of the computer? I ask because I've done that - had stories vanish only to end up somewhere else. But I've also had stories vanish never to be seen again :P