When you send audio from a Final Cut Pro sequence to a Soundtrack Pro script, any edits performed by the script are destructive —in other words your media files on the hard drive will be permanently changed.
A good way to edit audio from Final Cut without destructively altering your source files is to send the audio to a Soundtrack Pro audio file project first. This will replace the audio clip in your Final Cut Timeline with a Soundtrack Pro audio file project, which can be nondestructively edited.
To do this, control-click the audio clip you'd like to edit, and from the shortcut menu choose Send To > Soundtrack Pro audio file project. Soundtrack Pro will open and create an audio file project based on the audio clip. Now, you may either perform your edits in Soundtrack Pro or apply a Soundtrack Pro script to the clip nondestructively from the Final Cut Pro Timeline.