To add another perspective (although the chances are low, still a possibility though).
The sender might not have properly sealed the boxes (or the boxes were not of good quality). During transit, boxes might get slightly crashed, a hole opened in the box, hence some items fell off. At an arrival destination, they observed the hole in the box, and re-sealed the box.
This might sound like a science-fiction scenario
, however, the receiver of the package can prolly check if such a scenario is applicable. (the condition of the box, if the same seal was re-applied or a new one added, indications of how the box was initially opened before re-sealed, coins bundled -or not- together with additional packaging materials inside the box etc. etc.)
If USPS keeps weight records at each checkpoint, then should keep pushing them to provide those to you.
I had an instance in the past, where I received a small box that was re-sealed in one edge/corner. There was a printed note attached from my national postal network, that mentioned that they received the package with a hole/opened and they re-sealed it. (fortunately, nothing was missing from the contents). I am international and this was an incoming parcel from another country, hence your case is different due to that everything was handled by USPS.
Really sorry about what happened to you & I will keep an eye out in case I see any of those coins around in the interwebz. I am looking forward to getting my hands on those new coins whenever you release them for sale.
Edit: I read again and realized that you mentioned that "two boxes arrived empty". Too much of a coincident then...
Edit 2: When someone dispatches many coins inside a box, bubble wrapping them in a way that no coins sounds can be heard, is a common sence...