If it is a plated through hole (or via), it may connect two or more copper layers together. Removing the through hole (or free pad?) will isolate these different layer tracks and the existing track will "repair" itself back to the normal specified track width. You may find that the sections of track adjacent to this through plated pad might also disappear -depending on its connectivity.
Experiment with EasyPC as its WYSIWYG especially if you have set up every layer (copper + non-electrical) to be visible. Keep a backup of the original file just in case. Generate the full set of new Gerbers (and Excellon drill files), then import the files into a free online Gerber viewer to see if you have achieved your objective. Best of luck!