@mitu Same things happens...no folders (all, nes, snes and so on) will be copied. Nothing happens. It´s really odd. And...it´s ONLY the config folder that this happens to...all other folders seems to be copied.
Wrote this script and ran it a few times now. Monitors rsync to see if it's running (rsync I guess is what's used to copy ROMs from the USB to internal storage). Would be super if the devs gave us some way to know that it's still copying ;) ;) but this works, and was only using about 0.5% CPU usage.
Maybe try it with emulation station shut down by pressing f4. Emulation station may be rewriting the game list files when you restart it.
@lostless That was exactly it! I even remember reading about this very same thing in the RetroPie wiki but had completely forgotten about it. Pressing F4 to close down Emulation Station and then transferring the respective files/folders over works perfectly. Thank you!