I am having a serious issue with Magento and I don't know where to begin trouble shooting. I had about 40 orders come through my site on Sunday (7/12/15). When I logged in yesterday morning I saw the orders and printed all of them out for shipment (order numbers 100001511 to 100001540). When I logged back into my site today all of those orders have been deleted and there are new orders replacing 1512, 1513, 1515, 1516. I have reviewed my payment processors (authorize.net and paypal) and have cleared payments for orders 1511 - 1540 and duplicated cleared payments for orders 1512, 1513, 1515, 1516. The second orders for 1512, 1513, 1515, and 1516 are shown in my orders list but the original orders as well as orders 1517-1540 are no where to be found in magento.
The only changes that were made to my site yesterday was the linking of the website to Shipstation which was installed through magento connect. I reached out to Shipstation and they replied saying that it couldn't have been there software as they don't send any signals to Magento that could delete orders.
If you could help me diagnose this issue it would be greatly appreciated. I have no idea how it happened or where to begin on diagnosing what caused it.