StagingPro is designed to create staging environments and not (at least at this stage) a way of pushing data to production. One of the challenges faced is that item indexes are changed for each BigCommerce store and this includes the order id.
This will in no way impact the work you can do on your environment. StagingPro has still kept the relationships between records intact and the same amount of data has been moved so none of your testing will be affected.
StagingPro will soon be rolling out a new feature which will resolve this issue.