This came up on page 2 below of my thread "Experienced Users". My understanding is that when you update metadata, it is only stored in Calibre's database unless/until you "convert" your files. When you "convert" then the updated metadata can be written into the "new" file. Then you can "Save to Disk" your files. Then when you rescan/readd your books the metadata would come from the book files so in theory all the folder names, etc. would be correct.
But, I am a VERY new user of Calibre and this is what I think I understand based on the posts in the thread below.
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