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@Aussiecubs - When you say the book folders are empty, do you mean A) there are no ebook format files (EPUB. MOBI etc), or B) there no files at all, not even a metadata.opf file? If the latter then that would be very strange - every 'book' in the database should have a metadata.opf in the corresponding book folder.
What is the state of the 117 books on your backups. If they are likewise 'empty' that would explain why you didn't get a query from GS regarding what to do about deletions (fellow GS user here). Which would suggest that these books have always been 'empty', or the format files were deleted inadvertently soon after adding via one of the Remove format options -- i.e. before you ran the next GS backup
If you have suppressed the "Are you sure you want to do this" message you wouldn't know you you did it, especially if you've given any of the Remove formats options a keyboard shortcut - e.g. I have Alt+Del assigned to Remove specific format from selected books but I don't suppress any of the calibre "are you sure" messages.
BR
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