If you've used the USB transfer method to copy your ROM files, then you'll have both ROMs on your sdcard - the method just copies the new ROMs. Delete the ROM files on you sdcard, not on your USB drive.
You can use the File Manager from the RetroPie system in EmulationStation to browse the ROMs folders and delete them or press Select in EmulationStation when have a game selected and you'll have the option to delete it.