Issue with copying between USBs

Hi 

I want to consolidate two USBS with different folders and tracks into one. I want to do this by taking tracks from both and merging them so they have all tracks on both.

the problem is when I export the tracks onto my Mac and then copy them back into the USB, it doesn't recognise duplicates and give me the option to skip, and I have to go through them manually which is very laborious. The only way it seems to recognise duplicates is moving tracks within a USB. And I can't copy over tracks from one USB to another. 

Does anyone know how I would consolidate the usbs without having duplicates?

Thanks