Find the fuse for the TCU and pull it. wait a minute or two and put it back in. Having your battery go dead does not break the MFM link. However it sounds like your car's modem didn't come back up right. It happens from time to time. As an alternate to pulling the fuse, pulling a battery cable has the same effect to reset the TCU. you shouldn't need to do anything and your should automagically reconnect to MFM when the TCU properly boots up.
2014 Blue Candy FFE
http://www.fuelly.com/car/ford/focus/2014/triangles/303811 (since this forum doesn't allow BBcode in sigs)