Thanks for the response. As of now, all I have to match is name. There could be potential name conflicts that I would have to resolved manually. 

Then it should be a fairly easy job for Workflow. You could go through the documents in the first folder and for each one, search for the ones matching the name in the second folder. Then copy field values from the first to the second document. Depending on how your duplicate names are set up, you could also check if the search returned more than one hit and flag the original for manual processing.