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@BetterRed Thanks for the reply. What you describe probably works, but it sounds quite dangerous and slow (I have a quite large collection). I was hoping that Calibre could just deal with the `orphan' authors and books by itself, rather than me doing it in such an indirect way. The information is there already, all Calibre has to do is do an import on the orphan directories, or move them to a new directory.
Regarding how I ended up with those orphans, well, real life happens. I don't normally mess around with the directories directly, but the book collection is many years old, and over the years Calibre has crashed (rarely!), my computer has hung while Calibre was running, file syncs have gone bad, and who knows what else has caused this. And then it took me a while to discover this database cleanup feature.
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