I understand your frustration. You are just beginning to learn about how to keep a reef aquarium. There is much to learn. Sanddune600's comments were good.

In this instance, you are worrying about something that is a natural process of tank recovery following a disturbance, rather than an algae problem that requires major eradication techniques.

It may sound unbelievable, but if you had left the tank to run normally during that week, the brown algae would have been gone anyway. The brown algae now growing in the Refugium is actually doing the job it was meant to do. Eating up extra nutrients in the water. Turning off the light in the Refugium is not a good idea. If the algae is growing well, I would not disturb it by replacing the Chaetomorpha. New brown diatomaceous and dino-flagellate algae would simply re-grow on the new Chaeto.
I have two questions:

What and how often are you feeding the tank?

What light is on the Refugium and is it RDP?
If you leave it alone and let it recover naturally it will reach a balance on it's own. As long as you are not overfeeding and, in fact if you stop feeding for a while, the organisms in your tank will eat up the algae and because no other nutrients are being added, the tank will reach a cleanliness that may surprise you.
Here is an example
On Friday we left town for a long weekend. I had forgotten to feed the tank before we left and we returned late Tuesday night. That's five full days without feeding. All during the time, my wife who is also still learning, kept worrying about the fish. I tried to re-assure her that all would be well. Her very first comment Tuesday morning when she awoke was "Have you fed the fish?" She came out of the bedroom to see the tank.
"Wow, look at how clean the tank is

." she remarked.
"Yes, and every single fish is still there and doing fine.

" was my happy response.
You are experiencing "problem after problem" because you are trying to control a biological system that you don't yet fully understand. Honest, it really can take care of itself and look good
if you leave it alone and let it do it's thing.
The next time you start to worry, or wonder what to do, please feel free to call me at the number below and we can talk through it. That's why my # is there.
Edited by Mark Peterson - July 15 2010 at 11:57am