Part of the problem may be in the idle control system.
If the car is idling very low and cannot get the alternator
spinning fast enough to get voltage above 11volts, you will
get the battery charge warning message.
I have also seen several alternator failures on 98/99 E300D's
lately. The average milage has been around 75K for failures.
I would have FJMB keep it overnight and cold start it the following morning with test equipment attached to monitor alternator output, voltage, and idle speed.