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Rebuild will only work with extra titles if the file and folder names are in the correct format and they contain the correct opf file.
If you have random files and folders, then your best bet is to create a new library and do an add books from sub-folders, one book per folder.
As for that permission denied error, that will be because you ran calibredb restore in a folder for which you did not have permissions to write files (maybe the calibre progam folder?) All it means that the restore report could not be written.
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