Just confirmed with our VAR that this is the expected workflow!!
So that it is clear, if you are using Plant3D and Vault and you or your clients must never change their mind regarding the naming convention of your Plant3D folders, because if you change the folder names or move files between folders "YOU WILL LOSE ALL OF YOUR FILE REVISION HISTORY" if you follow the expected Autodesk workflow! Even more exciting, if you do not follow the workflow, you will be faced with the corruption of your Vault or Plant3d or both.
Vault was pitched to us as the tool that would solve the issue of having folders of historical versions of files (70%, 90%, FINAL submittals, etc) but instead, use the built-in revisioning of Vault to store all of these important revisions. This all works somewhat well and fine, until real life steps in and any sort of change in name occurs to your folder structure.