Cannister Filter = closed system
What goes in comes out
If you are concerned about build up, no worries. I've been running co2 directly into the intake of my cannister filter for a year. Very occasionally I get a slight build up of co2, but it eventually(after a few minutes) gets big enough to become "unstuck" and pass on through. This happens *maybe* once a day and isn't noticeable unless you are standing next to the tank. Additionally, it's not a large amount of co2, and it doesn't harm the filter.