Basically, when you know something is dead or on it's way out, you should remove it. Part of the cycling is helped by die-off, but if you let it go too far the die-off will cause more die-off, which will cause more die-off, etc... IMO, it is good advice by TBS to do water changes during cycling with their rock to keep things alive (it is common for recommendations of not changing water during cycling, but that's when there isn't much of anything to loose).
As far as the turkey wings and the rock oysters go, I have lost very few after a year. I lost pretty much all of the tunicates, but after starting to use DTs they have started to come back. If I did it again, I'd give DTs a try sooner.