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You are confusing Virtual Folders with real folders. Sigil now shows virtual folders by file type not actual folders (although they can be the same). Think of virtual folders as groups of files by type
So try your move again with a fresh copy. Before the move hover over the file in BookBrowser to see its book path.
After the move is done, mouse over and hover the file in BookBrowser to see its new full book path and not just the name.
If you want to see full book paths all of the time, enable them in Sigil Preferences.
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