Assuming there's a consistent structure to the workbooks, there is undoubtedly a way to do such comparisons and, so, identify the differences. Without actually seeing some representative workbooks, it can be difficult for anyone to advise on the specifics. Can you attach a some representative workbooks to a post with some representative data (obfuscate anything sensitive)? You do this via the paperclip symbol on the 'Go Advanced' tab at the bottom of this screen.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]