Other than a tool used to catalog your files (such as Lightroom) which would likely use a completely different file organization structure, I am not familiar with any tool to compare files AND subdirectories for said file.
Also you run into the possibility of two files having the same name. The "tool" would have to compare them to see if they were really different and know what to do in that situation. Time/Date stamp is helpful, but not always accurate.
That's asking a lot of a tool.
However, do you keep a backup of said pictures? if not, you should. Your computer's hard drive WILL crash. Guaranteed. Its just a matter of "when". Could be today, could be 20 years. But it WILL fail. Tools like Google's new Photo's app will monitor a parent folder and upload pictures to your Google account. It will automatically sort them by date, and not bother with duplicates (if same name). That might be an alternative option. From the Photos online you can choose to share them to people easily too.
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Albert
My Toy... is actually a 1973 Camaro LT and a '09 HD Dyna. 
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