If you send the box contents to Amazon, then the number of boxes changes, you will return an error worded something like: 

"The number of boxes in the uploaded file does not match the number of boxes provided in PutTransportContent."

You can download the corrected box contents by selecting the shipment and pressing the "Download Pack List" button in the purple toolbar and then upload the corrected box contents to Amazon.

  1. Download your pack list, making sure to select "Reset Box Content Source and Download"
  2. Upload to Seller Central