I have a report based on .unv which in turn is based on a BEx query. I need to update the universe to retrieve objects I recently added to my Bex query. I am facing the following issues while refreshing the universe structure through Universe Design Tool.
- When the option ‘Delete Obsolete objects’ is checked in the update wizard, UDT closes out. I then have to restart UDT.
- When the option ‘Delete Obsolete objects’ is checked, UDT hides almost all objects and classes with the exception of 1/2 classes and affixes ## before their name.
I am attaching a screengrab after the refresh is complete when the ‘hide obsolete objects’ option was checked. This may help you make sense of the error. 
The same issue has been reported in this thread. http://scn.sap.com/thread/3374159
I understand I can create a new universe on Bex query and copy the new objects onto my existing universe. This way I wouldnt have to deal with refreshing structure of the universe. However, I need to find the cause of this issue and see if it can be fixed. I am using BO 4.0 SP5.
Thank you.