Problems with Invoicing of modified intercompany purchase orders

[BE-IT]

Hi all.
We are using in intercompany process for consignment warehouse (A warehouse in a dummy Company B where Items are stored which not belongs us and are only invoiced after we consumed them in Company A). As we don't need any financial posting in the dummy Company B we just deletes the intercompany relation in the PurchTable in the Company A after we received the items from Dummy Company B. This process worked fine till couple of days ago.

In some of the delivery steps only one part of articles was delivered from dummy Company B. The purchase order in Company A was posted as usual with an packing slip. Couple of weeks ago we got the information that the missing item will not be delivered anymore. We deleted the intercompany relation as usual and deleted the item from the purchase order. The status jumped on received.
Now when we try to post the invoice for the purchase order the posted packing slip is not assigned so the Total packing slip matched amount under Matching Details equals 0.
Also the "Packing slip quantity to match", "Inventory quantity to match", "Unmatched Packing slip quantity" and the "Unmatched inventory quantity" are also 0.

Setting the intercompany relation between the companies is not successful.
Does anybody knows how we could post the purchase order?