I had similar issue appearing to me, I created the Purchase Return with inventory return and posted the return receipt, the inventory is reduced, and can see in inventory module, but what I found that upon clearing the supplier balance I couldn't see the purchase return I made. table POP30300 and POP30310 both has the records. Everything is good except the PM transaction is missing. I am doing workaround to create credit note and then apply, then delete the GL batch to avoid duplication. This is really a problem and never sorted out.
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