Interesting. What it comes down to is that both alternators together are not strong enough to provide the current required to retract the gear. So when you retract the gear, the battery chips in and gets recharged later. Unless the battery is flat, in which case the voltage gets too low for the FADECs to keep on running.
General lesson: if your gear retracts electrically (not hydraulically) or if you have other transient electric loads that are too much for your alternators alone (de-icing comes to mind), don't take off with a near-flat battery. Unless you and your aircraft like flying with a temporarily non-functioning electrical system.
The thing I'm wondering about though is, on a DA-40 (single) there is an ECU backup battery which gets used automatically if the engine master is on, but no current from either the main battery or the alternators gets to the ECU. And this ECU backup battery is protected by a diode and relais in such a way that only ECU B can use it, and only if there is no voltage on the ECU bus (or if you pull just the right combination of circuit breakers), so you can't run this battery down. Doesn't the DA-42 have a similar system?