Cleaning chamber 2 causes extreme cloudiness

[91mini]

I have chamber 2 filled with Cheato, filter floss and chemi pure. The walls of chamber 2 get very gunky and I need to clean the green and brown gunk off every once in a while so that my Cheato is getting light. When I clean the chamber it always clouds up the tank. Todays clouded the tank more than usual and got me wondering. Is this safe? Will the fish get stressed? Am I introducing any negative algae or malicious material in the display from cleaning this junk off the wall?