The bag would never be in the bag store in the first place!

Let's say for the sake of argument that BA123 to Timbuktu departs at 10.00AM. The baggage team will start "building the bins" at 07.00AM (roughly, I can't remember the exact timings) and will close the flight at 09.30AM (again, roughly).

The bag store will start releasing whichever bags it holds from 07.00AM, starting with the first bin that is opened by the baggage team. Again, I can't remember which bin starts first, but let's say it's Economy. The Bag Store will start releasing Economy bags, sending them down conveyor belts to the appropriate lateral. If, at 07.30AM, an Economy bag is checked in at front of house (or arrives from a transfer flight), this will go down to the lateral. It might do some "circling" if the lateral is busy, but it shouldn't go to the store. And so it'll be for the other bags until, at 09.30AM, the bag store is empty. There's no chance that any bag is "left behind"... I mean, something might go wrong in the extraction from the store shelf, but that would be a mechanical failure of some sort and a weird one at that.

If there's a bag for the BA123 still in the system at 09.31AM - "caught up in traffic", if you will, then the system will spot it and do the reflight I mentioned.