I have seen many blogs regarding this message. I had the same message and was able to figure out the solution, thought of sharing if this might help anyone.
Environment: SAP BI Platform 4.1 SP 06 Patch 4
Having 2 objects with same name in one class.
Refresh the Universe Structure
Check the Integrity
Change the name or
Place one object in different class
Export the universe and it works fine no more issue.
FYI: I see that this is resolved in SP09 for 4.1