I am running SQL Developer 3.2.20.09 and when i select a package in the navigator and select "Run" it takes me to a Run PL/SQL window. When I manipulate the code to be executed and run it, the next time I go to run that function, the modified code is retained. I see a "reset" button but it does not clear the change and refresh the code to be run from the package as it did on my initial run.
The Reset button works during any given instance of Run PL/SQL to return it to the state when that instance began. All modifications persist across instances of Run PL/SQL on the same package during the same SQL Developer session, so any changes not reset are cumulative during your session -- generally a useful thing.
Exiting and restarting SQL Developer will return you to the original state.