I don't know much about publishing, but I would think each department has a copy of their respective contributions. If I liken their editorial system to version control, why wouldn't, say, the art department have layouts on their local machines?
It isn't so bad, they did manage to recover the content:
"But all is well, he said, and the magazine will go to press on schedule next week. The recovery was made much easier, paradoxically, by a bane of modern business: litigation, or at least the fear of it. "The text had all been copy-edited and sent off to the lawyers, so it had been saved as e-mail," Quittner said."
They had a backup server. Misplaced automation is the villain. Makes sense to automate a task that you do 100+ times a day, but backups are generally run once a day, and are recovered maybe once a year.
My backup system involves a script with a bunch of copy commands that I can see flying by in the console as they work.