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It's not the metadata/TOC, it's the actual database and what will end up as orphan files as the file structure has changed. My understanding is that although the Forma 'sees' the current version on the Forma, when it syncs with Calibre, the updated file isn't recognised as being on the device.
The trouble is that I've cleaned up every file in Calibre which is why in some ways nuking everything and starting over is potentially a good idea.
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