I wouldn't. If you are doing fishless cycling, you don't need to do a water change or anything, unless water parameters get terribly bad!! (Of course you would want to do a water change before you put anything live in there.) Of course, others may have a different opinion, but I never clean a filter while cycling. Your good bacteria live on all kinds of surfaces, not just the biological media, so I like to take complete advantage of that.
There will be exceptions to "my rule" of course.....lol.....but in general.....