Isn't there a board or site somewhere that explains what "they" are doing when changes occur in the project that affect the donors in significant ways?

There is. You’re on it. But it seems that Rosetta@home has been so successful for so long that “they” no longer feel any need to come here. The supply of computing resources appears to be taken for granted. Researchers simply throw tasks over the wall; as far as we know they do something with the results afterwards. That a batch of work can get sent out configured in a way that cuts off a third of the project’s capacity, without anybody noticing or taking any corrective action even though the problem was instantly noticed and reported by participants, leaves it quite evident that nobody is actively monitoring this project.