I don't run Chaeto or an algae scrubber so it's hard for me to give advice on them. What I do know is that Chaeto can and will outcompete a lot of other algaes for nutrients which is why people love it so much. If it's doubled in size, you're getting nutrient export.
I've heard people talk about "false readings" when the Chaeto is in the tank still. I've been told that if you take half of the ball out, it takes the nitrates/phosphates with it. To my thinking, that doesn't seem accurate. If the nitrates are in the Chaeto, they won't register in the water column? But I'm not a scientist and I don't understand that part of it. My guess/theory is, when you harvest Chaeto, the smaller clump grabs a bunch more nutrients to grow back what you just stole.
Either way, if the Chaeto is growing you're getting nutrient export. Are you seeing a lot of algae in the DT?