You may have an extra mountpoint created for the hard drive.
First look for extra mountpoints. From an ssh session into the batocera machine, check that the /media directory only has 'Recalbox-Media' in it. If it has more directories (Recalbox-Media_1, Recalbox-Media_2, ...Recalbox-Media_n) you will find that your external storage has been mounted at the last one. If there is only
Recalbox-Media in the /media directory then this is not the problem.
If you have more than one Recalbox-Media subdirectory in /media then do this and I think you will fix it:
#umount /media/Recalbox-Media_n (where n is the last of the extra directories)
#ls -l Recalbox-Media_n (make sure the directory that you have just unmounted is empty.)
Then, after the /media directory is empty:
#shutdown -h now
Once the system shuts down, restart the system and see if it is fixed.
!!Nicholas - I am getting a security violation on this site in chromium because your certificate has expired.!!