In ProTools, AudioSuite Plugins have a button that says "Use in Playlist". When this button is ON, the new file created (with effects) replaces the old file on the playlist. If this button is unchecked, the new file will only be placed in the Regions list, and not in the Playlist.
You'll also want to be sure that the top-center button in any Audiosuite plugin says "Playlist" and not "Region List."