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You can export all books from each library (by doing "Save to disk"), and then import all books into a new, empty library. This will preserve all tags etc. If the overlapping books are identical (same files), you shouldn't lose any files.
Be careful if you have any files that are not on the list of supported extensions (pdf, lit, epub, txt, zip etc). If you added a file that Calibre doesn't recognize (like a .tar file, for example), then it will be saved during the export, but it will not be imported into the new library.
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