The warehouse runs on a second system, and by Friday it and the ledger disagree about the same shelf
Neither system is wrong. The warehouse system knows the bins, because that is what it was bought for. The ledger knows the value, because that is what it is for. Each is right about its own half, and the half they share, how many are actually on that shelf right now, is held in both and owned by neither. So the count is done on a clipboard, keyed in on Tuesday, exported on Wednesday, and the two numbers are compared on Friday by a person whose job that is not. The variance is always explainable. It is explainable every week.
What changes with inventory and warehouse
The Friday reconciliation stops existing, because the second number it reconciled against stops existing. On-hand quantity is one record, held per location, per lot, per package and per owner, and because the ledger moves with it, the warehouse and the books read the same shelf instead of arguing about it.
A count is entered against what the system already holds, and if the stock moved while the count was open, that surfaces as a conflict rather than being written over the top. The one thing a person is asked is the count itself, not to be the integration between two systems.
Where a pallet goes when it lands, and which lot leaves when an order picks, are rules on the location, resolved in a fixed order, not decided by whoever is on shift.