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Sounds like her library got messed up. Is it on a networked drive? Is it being synced with Dropbox or something? Has the library been moved to/from different operating systems?
Networked drives are a BIG no-no.
Dropbox and other methods of syncing cannot be run while calibre is running, or they may argue about where files are. (Everyone loses.)
I doubt this would be the problem, but the database cannot reliably track files when moving from a non-case-sensitive OS to a case-sensitive one.
In any event, I suggest she try Library Maintenance ==> Check Library (from the dropdown by Switch Library) to see where the errors lie.
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