I see that one of the system in my WB project is corrupted and I cannot either delete it (when I delete it, the entire project is gone)
Here are the steps again to delete a corrupt system from the WB.
badSystem = Project.GetSystem("SYS 3")
badSystem.Components = 
If everthing is working well, ignore Step 4. If there is some problem saving, then close the project and try Step 4.
Save notepad file. Then you could open the project again.