I've had mine now for a little over a year and about a month ago I did just that - rotated them (we flipped the mattress so thought maybe I should rotate the squares ). But to be honest they seem to be holding up really well. I've not noticed a difference or a problem.
Hey I think that is a good idea about switching the mats around!!
About the question on the wear of your puzzle mats. I would think as long as you are not having any problems with your knee's. I would not replace them.