How do you compare multiple folders with same files to find all different versions of the same file?

Use git and a script to create one branch per folder in a single repository, then have the script try and merge them all into one. You'll be notified everytime files differ.

You could start by using a program like dupehunter to reduce the structure to the really differing files (of course you should start from a copied folder structure!). Then WinMerge can at least compare two folders.

What you're looking for is a File Synchronization application...

DirSync Pro is my personal favorite

Note: I know the 'pro' makes it sound like the average half-baked proprietary marketing crud but don't let it fool you. DirSync Pro is free, open source, and cross-platform

::wagging finger:: And, I hope you learn't your lesson from this debacle ;). Get those files under revision control and branch if you need multiple concurrent versions of development.