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The real problem seems the mass of books in the libraries with more or less identical content. And this will go even more problematic with every day lost not make a break with this kind of management. If he really want to get rid of this this situation he need to stop this kind of management.
I would suggest to conflate the libraries in one library. Doing this without loosing information in an uncontrolled way use a custom field/column in each library that identify the source library (e.g. Lib A, Lib B...). This field will take care that data sets won't merged together during the import.
After all books are imported you can use this field to identify your work sets and as well as status information for your clean up process over the time. In addition you will be able generate to every time a single subset like your old libraries as physical or virtual library by using this field in a search rule.
Define the field as comma separated text like tags and you will be able to assign a book to more than one library / status and what ever else you need during the cleanup process.
In addition you can take a look to some of DaltonST's plugins too. He have some really powerful tools (depending on how experienced you are in defining search constructs with database tools like SQL).
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