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 not impact the work you can do in your environment. StagingPro has still kept the relationships between records intact and the same amount of data has been moved, so none of your testings will be affected.
StagingPro will soon be rolling out a new feature which will display the original order id from the source environment in the Order Comments section of the destination store.