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calibre does not touch the library folder when it gets upgraded. The problem is almost certainly unrelated.
Is your friend by any chance running any file-syncing programs on her library folder?
Dropbox, Google Drive, SugarSync, Copy.com, Time Machine all qualify.
If so, she should never run any such service while calibre is running. The two will disagree on what goes where and you will end up with files/folders getting reverted, deleted, moved or assumed moved, etc.
When you edit title or author data in calibre, all affected books are moved (on the filesystem level) to reflect the new names, which is when the disagreement starts.
You can repair the damage by looking at wherever the backups are kept, for Time Machine, or by having the Dropbox/whatever team rolling back your cloud to a previous time. (You will lose all changes since that time.)
She can confirm this as the problem by running Check Library instead of Restore database. I suspect she will see a long list of missing files, and possibly some extra ones too.
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