I always harvest the yeast from the primary and discard the yeast from the secondary. This is mostly because I only use a secondary if I am dry hopping. That said, I still think you want to use the yeast from the primary. The yeast that is left when your beer gets to the secondary is less floculant. If you continue to harvest from the secondary it could cause your yeast to become less floculant over time......I think....I don't really have first hand experience with this though. I wouldn't think that harvesting the yeast from the secondary this time, then getting it from the primary from now on wouldn't hurt anything though.