Shawn,
Most parasites have a life cycle that one must understand.
This cycle is dependent on temperature and can be a few days to many weeks.
If there are no fish present when parasites hatch they will perish depending on temperature and time.
Some parasites like fish lice have such a long cycle that it will be difficult to eradicate them by just taking the fish out, but it is a very obvious thing and anyone will be crazy to use activated sludge from a pond with an anchor worm or fish lice infection
It is also suspected that some parasites (like costia) can encyst if there are no hosts and can remain dormant for a very long time.
Anyway the technique that I describe is a valuable technique and I have not experienced problems.
Like doc Johnson said "Parasites are not a disease" and can be treated very easily
He recently made a video on KOI BEGINNER about this subject. You may find it usefull. http://www.koibeginner.com/video_bioseeding_koi_ponds_cycle.html
Keep well