Stock Tracking on Online Ordering
Have the stock tracking and limitation for Online Ordering, therefore if an item it out of stock it will hide on the online ordering to prevent customers from selecting that order.
Grant Strayer commented
I'm having an issue where all my modifiers are being marked as out of stock, I believe it would be related to this idea. I've called support multiple times about this and they recommended I post here.
After stock is depleted, items should no longer be available to purchase through online ordering.