Just an opninion here, since I've never done a CBS league.
Somewhere in CBS's systems, they must have the ability to recreate your roster from "x" amount of weeks ago. I know in Yahoo leagues, if you look at the final score of a H2H week from, say, 5 weeks ago, it will only show the players that were on your team at that time. Any players you have added since have nothing to do with the record of your team from week 13.
They will add Jeter, Cano and Arod's stats to the week 13 totals and recalculate them. Maybe you'll still lose, maybe Arod will have a monster game and you win. Either way, Markakis' extra stuff should get added to whoever had him during week 13.