I found an indirect solution in https://stackoverflow.com/a/3634631/1443563
To delete all data on development server, issue the following on cmd prompt:
/path/to/google_appengine/dev_appserver.py --clear_datastore yes myappname/
where myappname is your directory containing your app.yaml file for the app
you need to cd to this directory path
This deletes the autogenerated indexes along with the entities
If anyone knows how to do this without deleting the entities, please share the solution
credit: Steven Almeroth and Melllvar