Current setup:
MainProject which is a Library Project
BranchProject which is a new projects and has MainPr
I faced the same issue while debugging the a .java file using Eclipse IDE. As per my understanding this issue comes when we put the xyz.class file of xyz.java file or JAR at the project build path. Delete the .class or JAR file from the project class path and rerun .java file in the debug mode. This time you see a source not found window. Click on "Source not found" button and check "Find duplicates..." at the bottom of the window. Done your problem is solved :)