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If a stock item does not arrive on a purchase order - count the received qty as zero = the purchase order will then be processed normally.  The  

The invoice will match up with the shipment

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Count the stock that arrived - the counted will be greater than the ordered qty.  The  

The system will prompt if the invoice includes the additional stock - or if it was sent as free stock

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Perhaps they were ordered on a previous purchase order that was short shipped.  Use  

Use the "Add Item" button on the stock receipt to enter the new item and qty, it will have a zero ordered qty - the invoice will be created for the counted quantity.

You will be prompted to make a choice about the "More Stock Arrived than Expected" as above.

The invoice is a different price each to the purchase order after stock has been counted and received

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