Good question. I think if you could guarantee which 1/3 you were tossing you could do it and it would probably be the best thing, consistency wise, you could do for the stability of your tank. UNFORTUNATELY, you'd be just as likely to keep throwing away the same 3rd of the media unless you ran 3 separate units on your system. If you want to save the media like that then I would suggest getting additional Phosban reactors. I run two (daisy chained) but in my second I run carbon.