When user runs Query Repository - Diagrammer Scopes or selects a Scope in Diagrammer, receives message "-2146233088 : Element wth key JAVACLASS doesn't exist" is getting displayed."  The actual element can be other entities besides JAVACLASS but the error message remains the same.

Issue is related to leftover and unused artifacts in the workspace after an upgrade or configuration change.  The correct resolution is to re-configure and upgrade the workspace.