Very Advanced Program To Copy Files ?

I have old backup of favorites (bunch of *.lnk files) from Internet Explorer that i had on cd and forgot about it. Then i formated my pc and had to start over collecting them.
Now after year i find out my old favs was on backup cd and i want to merge my old favorites with my current ones, the problem is there is about 100 links in old folder and about 200 links in current folder and many of them lead to same sites, i dont wanna have duplicates and i dont wanna sort them manually.

Is there prog that can copy file from one folder to another, checking if each file from source folder is not present in destination folder (and subfolders) under different name (by checking size or crc or md5 whatever)?

Or prog that can check which of files from source folder (without subfolders) are same as files in destination folder (without subfolders) and mark them to delete or move or smooth