I think I understand your question as what you are talking about unfortunately happens all the time. The part was shipped at the old value of zero, so you have a wash on the shipment, which will make the invoice look like it was 100% profit.
When you receive it off the job, then it updates the average cost in the part cost table, creates a debit to inventory and credit to WIP to clear out the job. So the net result is your inventory value will be out of balance since you shipped a zero value part before it was received and now you have a debit balance in Inventory with no quantity to match it.
The last part of your question is yes, if a part has a negative balance, it will value it based on the current average (or any) cost. I am surprised the last cost was not updated when you recieved the inventory from the job. Not sure why that would have happened.