As mentioned previously, Retail 365 offers you a few options on how to handle checking in items that have a difference in the quantity sent and the quantity received

If an item is marked as backordered or flagged it will automatically appear in the 'Flagged Deliveries' tab

How to resolve Flagged Deliveries

For your own records, it may be helpful to mark any flagged deliveries as resolved once the stock is recieved instore from another order etc.

This can help you to keep a record of any flagged items and manually add them to an order if necessary

Select the flagged items from the list displayed in the 'Flagged Deliveries' tab and click the button