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If you don't maintain personal metadata (read status, rating...) in the Master Library then those columns will be 'empty' - you may want to exclude some columns (e.g. ratings) from metadata downloads.
When you send a new book to His and Her Libraries they will still be empty - then its up to Him and Her to maintain the personal metadata (read status, rating...) in their respective libraries.
But do you actually need to retain books in the Master Library. Why not use it as a Receiving Dock where you do deDRMing, adjust author names and title, download basic metadata, do conversions before copying it to His and Her libraries and then delete it from the Receiving Dock.
To safeguard the personal metadata you should back up the His and Her Libraries individually . So Her backup could be a secondary backup for His Library, and vice versa. Most book files (format files) aren't that big, so having similar backups is not normally a big deal.
BR
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