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That doesn't make sense. There's something in there that you think you're doing but you're not actually doing.
Try this to workaround everything:
Use the Switch/create menu action to create a new empty library, in a completely new location,
now in the new library, click the arrow next to add books and select add books recursively, one per directory.
Choose the folder containing your old library.
calibre should re-add all your books, preserving their metadata.
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