Mud isn't scour. It is excess sediment carried by the stream and dropped when velocities decrease enough. The excess fines (coarse sand on down to clay) smothers the eggs regardless of whether or not the flood scoured redds.

Also, lower flows in the fall force fish to spawn in the thalweg, the line of highest velocity. All the fish forced to spawn there put their redds right where the most scour will occur of there is a freshet.