Why is my line 42000 Net federal tax the same as line 40600 federal tax when I have almost $6000 on line 35000 for Total Federal Non-refundable Tax credits?

Line 40600 already has the amount from Line 35000 removed (See steps 127 to 130). You would have to look at steps 139 to 147 to see why there is no change between the two lines.