There is a known issue with drives of 2TB and larger, If i remember correctly you can re-format it in advanced -> developer -> format disk. Make sure you format only the disk with batocera and not any other disks, so that you do not accidentally lose any data that is on the computers internal harddrive.
I think the newest beta also has fixed this issue. Maybe safest thing is to burn the newest beta and then downgrade to stable?
Another way is if you are familiar with linux is to use a tool like gparted to expand the drive (share) to use the whole drive.