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How can I compare two directories to compare missing files, when the directories don't have the same structure?

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http://serverfault.com – I've been sent a HDD of new and updated files from an organisation that we are working with, but we already have most of the files sitting on our servers, and would like to update our local versions to match theirs. Normally, this would be a job for something like rsync, but our problem is that the directory structure they provide is very poorly organised and we've had to rearrange their files in the past to work best with our systems. So, my question is: How can I find out which files in the set they have provided are new or different to the versions that we have, when the directory (HowTos)