Manage minor leagues in franchise

[cch25_XBL]

So I started a franchise with a fantasy draft, and at the end of year 1, I lost nearly all of my minor league players, and the franchise automatically sent down all of my MLB players to fill in the vacancies in my minor league system. Do I have to manually re-sign all of my minor league players? Is there a way to let the CPU handle all of my minor league affiliates so that this doesn't happen? I hope this makes sense, let me know if you need me to clarify.