I've had similar issue with that build, I think it's something to do with the partition that is created to save the settings and store your ROMS. If you plug it into a Windows box then it may get corrupted by Windows or the EXT application you are using is corrupting something on the drive. I have random boot issues with that build, usually after changing preferences in the menu. Sometimes resets to default and loses all settings.
The boot drive is a squashed file system and so does not store any settings so will not have any issues booting after a crash from corrupt or locked files (apart from the recalbox-boot.conf file in the root which can cause a boot failure if not set correctly). The system will boot to default if the shared settings drive or partition is not found or corrupted.
From my experience, you will run into problems if you decide to try copy files over manually from a Windows box, the system is tightly configured to use Samba and network shares for ROM transfers. Using 3rd party apps and mounting drives in Windows will usually leave you with a corrupted or problematic disk.
Although the idea of using a USB stick to store files is much more preferred as it makes backups easy and can also use the stick in other machines. But as you have found you will run into problems at some point which I think is caused by file locking and locked files left on the drive after a crash, which can prevent Batocera fromm booting or reading/writing the files on the drive.
What utility did you use to burn the Batocera image ?