I would add that if you look at all the budgets for the funded councils, you will see that there are several other components that have been added to the councils' programming. I would also stress that for the $50 million you are referring to, there were no cuts to what is called "fundamental research". It was other activities that were eliminated.
However, there have been additions in various other areas, so the total of the budgets allocated to the funded councils is higher.