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are you saying the when sorting by date in calibre and in stanza you get a different ordering?
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Yes, that is correct. I normally order them by date as it is easiest to work with them. I can understand how the majority of them could have a new date as I rebuilt/re-added then to a clean install of Calibre as you had suggested. It seems as though the newest books I just added after that are not showing correctly. I've just run a database check and did find a few empty folders but not enough to create this same error. I've also verified via the tags that they are in epub format.
Beau