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I created 2 files with 3 sheets each. The first part of the workflow loads the filenames with a directory tool, then loads the list of sheet names for each and then uses a simple batch macro to load all the sheets from both files.
The second macro then compares sheet by sheet and writes the differences to a new file called differences.
You'll probably have to modify the unique tool and join tool in the find differences macro to work with the column names in your files. I didn't look into making this dynamic. Perhaps replacing these 2 tools with the "Only Unique" Crew Macro will make it more robust.