I used this protocol yesterday and some of the BBA is turning reddish. Not all though, so perhaps this will require a couple of treatments. I will space them out by at least a week or two.
I did not turn off the filter and I did not take out the media. As predicted, the biofilter took a hit and I had some ammonia this morning. Nothing that a 50% water change didn't fix though. Next time I will unplug the filter and rely only on the powerhead for flow.
Fauna are fine although they did show a bit of distress around the 13 minute mark. My livestock consists of: