There can be a number of reasons why the stock in AGR does not match the stock in the ERP:
This could be due to a stock transaction that has been posted to the Item Ledger Entry table (BC) or appropriate transaction table for your ERP since midnight. AGR takes a snapshot of the data at that point, so if e.g. a purchase order was receipted after the snapshot was taken, it will show in the stock the next time AGR updates data (tomorrow).
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Is the ERP stock considering the same location(s) as AGR? You can see which locations AGR is considering in the Locations section of the ERP Settings, accessed via the Navigation bar:
For BC/NAV ERPs, if an Item number is changed, it can cause discrepancies in the Item Ledger Entry table and therefore cause incorrect stock quantities to be presented in AGR