All quantities are updated by Purchase Orders when posting the Receipt. Running Day End in PO is not necessary to update quantities.

If the sum of the quantities from all locations does not equal the quantity on hand for the item, there is no 'qty shipped not costed' values for the item or locations, and the integrity check does not find nor repair the difference, then the data is corrupt and needs to be repaired.

You probably want to get your Adagio consultant involved at this point.