Is there a way to delete meta-data on Eclipse run configurations?

Open Eclipse. Follow Run => Run Configurations. You will see options on the left hand side. Under the Java Applications option, you will see the list of runnable classes (the ones have a main method). These class nodes on that list are right clickable. By right clicking on your running configuration, you will see New, Duplicate and Delete options. You can delete your old running configuration via delete option. To create a new running configuration, right click on Java Applications option and click on New and then configure it.

AFAIK launch configurations are stored on:

${WORKSPACE}/.metadata/.plugins/org.eclipse.debug.core/.launches

Take a look to the existent configurations and remove those that are not interesting to you.

And restart Eclipse