[Inferno]

Just an idea as space is the only issue and you want a "library" that is the sum of all your libraries. Lets call this one Catalog.

Make a merged version of your libraries while keeping the original libraries safe on your external drive. With the merged library (Catalog) temporarily taking most of your drive space, selecting all books delete the "epub" files using "remove files of a specific format from selected books". Repeat this process for mobi, azw, pdf etc.

This will leave you with a library that has only the metadata info and not the books.

You will need a field that indicates a book needs to be added to the catalog in your other libraries.

I forgot to mention that this catalog should be considered a "static" record of your other libraries. You should not update the metadata of the entries as the metadata of your books in their individual libraries will not be changed.