Keeping the water won't really matter, as the bacteria needed don't generally stay in the water column. Your tank may or may not cycle again, but there are a couple things that will prevent this. The easiest is just to not clean the filter for a couple/few days prior to your change. I have done this several times and never had a cycle or mini-cycle or any elevated readings (I generally test daily for about 2 weeks after changing substrate). If you are really concerned, of your tank is slightly overstocked, you can do your change in sections rather than all at once, though I find this more difficult and cumbersome and just don't bother with it. Good luck!
\Dan
