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Originally Posted by BetterRed
I was planning to get the OP to run the Check after the Restore; there may be some books that are recoverable and others that are not recoverable.
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I suggested running it first because a) it is quick which restore is not, and b) if it doesn't find errors then restore won't do anything useful. If it does find errors then they can be instructive. For example, "Extra" authors are folders that don't contain syntactically valid book folders, which probably indicates external tampering of the library. There is something similar for title folders, checking the syntax of the folder name.
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Does Restore destroy unrecoverable book folders - e,g book folders with no metadata.opf? I've never had to run it in anger.
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Restore doesn't delete anything except metadata.db, which it replaces. The old database is saved as metadata_pre_restore.db. Restore checks several things to be sure that the folder structure is semantically correct. The check involving metadata.opf also checks that the book ID in the containing folder name matches the book ID in metadata.opf. If it does not then the folder is ignored (and reported as ignored).
Perhaps the best solution is to back up the library then try restore. The list of errors might be instructive, and the library can be recovered if needed.
Another option is one I think I have seen you suggest: create a new library, do a "Copy books to library w/delete", then see what is left behind.