Hello,
There shouldn't be an issue with charging the batteries per se. However if the battery completely dies in the MC3000, then all that data is lost at that point. If then the unit is charged, it will look like the data was lost when the unit is brought back up. Alternatively it is possible that you have a faulty unit and it is self-cold booting during charging. A healthy unit will not lose our software during a routine charge.
Thanks!