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I assume that all books have the same metadata on all computers. But all books are not on all computers.
If that is the case:
Use Save to disk from all three computers, and save all formats to a simple structure similar to the normal structure calibre use, one book per folder with several formats.
Make sure you use the exact same save template for all computers. Save to the thumbdrive and save to the same folder, so duplicates overwrite.
Then create the new library by adding the books from the thumbdrive, one book per folder. And read metadata from the books, not from the file names.
This should make sure that all books are in the new library, without any duplicates.
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