I have the same problem about copy tree Tools.It means when we use it for do not design whole SubAssy , Assy and Parts one more time from begining in new project .
But result of Tree copy have these faults
1-In new Project all files linked to previous project and you can see in their Data Card
2-New project No is not effected on files and you see project No. belong to previous project
Do you have any solution for me?