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@ChipAhoy - looks like something on your system is either, changing the file attributes of the metadata.db file in the library folder, or changing its permission settings or those of its parent folder. I've no idea what that might be. Pretty sure it wouldn't be calibre though. Probably the OS itself, or 3rd party security software. Which version/editions of Windows are you using?
You could use File Properties to examine the file attributes and permissions (Security tab) of the metadata.db file, that might give you some clues.
BR
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