It was me.
I have done disasters before and know how to add new species. I am getting better at checking what's still alive and whats not based on the effected zone. In short i believe all species that went extinct are, but i could always have made a mistake. In fact during it i made a mistake and started to change the wrong river. I started to change Irinya River rather than Ichthy River. But i fixed it. Firefox search button works great for finding species quickly to make sure they still exist in other biomes.
I left some at the brink, while others i made extinct such as the Pink Xenobee. It depended upon the Sugar-Trunk Bubblearch and thus were symbolic to each other. So once the bubblearch died it went with it. Also the Flisch River ecosystem pretty much collapsed beyond repair and many smaller species died as well since there was no other smaller food for them to eat.
Some suggestions are evolving some immobile plent trees from the Tropical Rainforest to move in and re-establish itself in the Temperate Rainforest and Temperate Woodlands. There are many smaller worms that feed on plants and that would really save them.
Also now with the chuts gone the large fauna niches are wide open. I am thinking maybe the sawtooth family could come in and take their place. Or maybe the Pipent could come down from the North can fill the void.
Besides the Chuts the 2 other hard hit groups were the blue palms which have very few species left Also the Brownble lineage and Snorkelcrest lineage. Ironically these lines I made so you can see that i pick no favorites when it comes to extinction.