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The folders with a number in the name are those that belong in the Calibre library. Any without numbers have been created by some method other han importing into Calibre.
The Save to Disk facility is used for when you want to export a file from the Calibre library. No need to do it as a matter of course. Sounds as if you used it and then gave the same location for the Save to Disk as your Calibre library and thus the duplication.
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