You need to read my thread elsewhere on this forum -
http://forum.a8parts.co.uk/showthread.php?t=13674
When the battery goes very low, it can [and does] lose the configuration of the Control Head ECU that runs the MMI. Your Control Head has lost all its settings and options.
You need to readapt the control head and also set the coding.
VCDS job , I'm afraid ...
Julian