I'ld rather have them both running and ready for when the next tank is ready. I don't want the CF1200 to dry out.
The CF1200 was cleaned out only week before last, so the bacteria is still rebuilding in the CF1200, especially on the sponges.
I was planning on this also. 50% to each tank, and rest filled with new dechlorinated water. Wasn't sure about the water carrying the bacteria, they like to cling to surfaces, or so I've heard.
If I disconnected the CF1200 and replaced it with the CF1000, there should be enough bacteria in the tank (glass, substrate, etc) to maintain the water parameters, but I don't want the CF1200 to dry out, and I wanted to prevent having a new filter on an old tank and a cycled filter on a new tank - it's two possible ammonia spikes instead of one.