Pretty simple bug, but one that silently removed most of my batteries!
What I’d been doing is keeping rechargeable batteries in a battery recharger trunk in my vehicle. I’d go up, press E, eat the ones in the trunk and leave, assuming the batteries would be freshly upon my return. As it turns out, (E)ating batteries from the player inventory depletes their energy charge (as expected), but doing it to ones on the ground or in a trunk simply deletes them.
Seems either way it’s some unintended behaviour?
Note: This only happens if the entire charge of the battery would be depleted.