I read it is possible to do a filename only compare between two folders if you set the time comparison value to a large number or possibly set it to be a negative value, which I see is a newer feature.
I am new to freefilesync. So how do you set this time variable? I can't find this setting in the GUI. I am on mac osx 10.9.
filename compare only
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In the Help files, check the *Expert Settings* page. It has all the information you need.