I have observed that after combat lost health is automatically regenerated.
However, it seems food & drinks consumables are used to regenerate that lost health. Which is why the food & drinks menu was often empty after some time of playing.
So, I don't experience a bug where food & drinks just disappear, but are rather consumed automatically out of combat. The codex entry for 'Food & Drinks' is a bit misleading as it states "manually" but there is no mention of it being automatically used.
Perhaps other players are experiencing the same with regard to an 'empty' Food & Drinks menu.
