Can one CHOICE run out while the dish itself stays available?

Yes — stock is tracked per option as well as per item, and both are opt-in. Track the choice that genuinely runs out (the last tub of saffron sauce) and leave the rest alone; the dish stays on sale and only that choice becomes unavailable. Renaming a choice keeps its count, because it is still the same choice — removing one and adding another starts fresh, because that genuinely is a different choice. A "replace" Excel import rebuilds everything, so per-option counts start again there by design.