You can exit EmulationStation and then, from the command line, run
sudo umount /media/usb0
If your USB drive is mounted on another folder than /media/usb0, substitute /media/usb0 with the proper folder name.
It's apparently the best solution... what i have do:
F4 to exit from ES.
mount (to found corrent usb)
used sudo umount
copyed all my news roms from pc and now also the image snap and some gamelist.xml from my personal system
type exit from console to restart es and....
@mppsan If the system you're copying to has also RetroPie, chances are the system is loading you USB pendrive in the ROMs folder and you're just re-copying the files on the usb. Disable the USB mount service from the RetroPie-Setup script and then mount the USB pendrive manually from the command line.