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I think it might make a difference if you have ePubs or kepubs.
kepubs, Kobo KNOW they can delete but leave the stats in the database as they can redownload them from the store.
Sideloaded kepubs I'm not sure what Kobo would do; they're not in the Kobo managed portion of the drive .kobo\kepub; rather they could ne anywhere on the file system.
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