Creating a photo master archive - how do I check I have all files?

I am creating a photo master archive. I have collected all the photos from many, many hardrives I have used over the past decade and a half, each with different folder hierarchies. In the master archive I am creating a folder structure based on the year, month and day the photo was taken. Almost all photos are jpegs.

I am looking for software which will help me to identify any photos I may have missed in this process - scan a hard drive and give me a list of files (photos) which do not exist in the archive. There are plenty of file comparison programs, but they presume an identical folder structure on both sides. Duplicate checkers sort-of help but this is a destructive process.

Any ideas what might work?

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