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I have a new setup and entered new products for which i updated the quantity on hand to reflect the real stock.

I put the cost strategy (Inventory --> Configuration --> Product Categories. / All) to Average / Automated.

But as i have entered the quantity on hand manually, there are no PO and the cost is not calculated.

Can i automate it so that the cost is updated equal to the purchase price for the corresponding product ?

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You can export the products (cost field only) and set the cost in the exported file and then import it again and the cost will be calculated automatically.

The export file will have two fields 

Id: Don't change it

Cost: You will update it with the purchase price, if you have multiple purchase price for one product you have to calculate the average as below:

average Cost = ((Qty1* Purchase price1) + (Qty2 * purchase price 2))/(Qty1 + Qty2)

It's better to so that in a test DB before doing it in the Live DB.

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This doesn't work. The file is imported as new items