Hello Aenoxic,
I just followed your steps to reproduce, and my placed ClassDesigner is still there.
BUT the ‘Tripod’ BaseMesh is now gone! To add clarification to this bug - do you mean to say that the “ClassDesigner BaseMesh reference is now Empty/Null/Cleared/Invisible?” (To me, gone/nonexistent/deleted are equivalent)
If you search the Outliner for ClassDesigner you’ll be able to see if they are gone or just invisible.
Thank you.