Does Walt know Todd can't cook it to be blue, though? All Walt knows is that Todd was having purity issues; the first time color becomes a concern is the first post-Declan cook, when Lydia is surprised it's not blue (which would seem odd if Todd had a known issue producing blue-colored meth from his first two solo cooks.)
Having blue meth hint to Walt that Jesse is still alive would be pretty effective narrative shorthand, but I don't think there's much in the show that establishes that's factually what happened. Had Charlie Rose mentioned the 90+% purity, I think it'd have been a more solid indicator.