It will still offer some filtering, though not as much as the other outlets. That may not be a bad thing as what filtering you do get may be all you need.
Having an integrated using one of two H/C slots I had the other free to use. My SACD player was supposed to go with one of the remaining outlets employing more filtration. I tried both high and low filtering outlets and couldn't, for the life of me, hear a difference.
Using both sounded equally great.
All the best,Nonoise