I fixed this by staying in the area of the resources for about 2 hours. This brought back the resources. I then set the resource respawn to 0.0. This will respawn resources instantly. It feels a little cheaty but as long as you don't give into temptation and farm the same rock over and over, it's ok. My guess is that nodes stop tracking time when the player leaves the area. This is very silly in a single player game.