Just a thought. Does the database not store a reference to every file (and possibly a filesize and/or checksum)? If so why not use that to validate the files?
There is NO network connection between them, and there can NEVER be a connection. (requirement of project)
Just to clarify more, do you mean they can never be on the same LAN? What about just the two machines with a simple network switch? Or even a direct connection between NIC's (I know there is a way to do this but I cannot remember the details).
Otherwise the quickest and probably the most certain is the hashing option suggested before. You can hash the ZIP files on both machines, then hash all files and push the results into a txt file (so you will have filename and hash value). Then run COMPARE from the command line on the two files. You should be able to do all this, excepting the HASH, using tools in the Windows OS.
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