In my case I deleted a project and re-imported an android application in the same workspace. But when I tried to set the run configuration (Right-click project -> Run As -> Run Configurations...) for the re-imported android application, the IDE threw an error saying - A 'Android Application' configuration with this name already exists - as in the snapshot below:
To fix this, all I did were the steps below:
1. Delete unwanted .launch files that represent stale run configurations from the location (<your_eclipse_project_workspace>/.metadata/.plugins/org.eclipse.debug.core/.launches/)
2. Restart Eclipse IDE (File -> Restart)
Alternatively, the simpler mechanism is to simply uncheck the filter for deleted/unavailable projects to make visible all stale run-configurations. The snapshot below is for your reference (you got to uncheck the second filter):
Hope it helps!