Sending fewer units than the shipment stipulates

I was going to send 500 units to FBA. Now, I want to sent 40 units instead (sending the rest to AWD). I already set up the shipment and labeled the 8 boxes with the 40 units inside. Can I just go ahead and send them to FBA? Will there be a problem simply resolving this as a discrepancy after the fact? Will this impact my account standing?