The only uncommanded engine shut downs I have been involved with were all but one preceded by fluctuating or surging rpm.
Any sign of surging RPM on a DA42 needs to be investigated by the techies, specifically to look for damaged wiring, loose plug, corroded connector pins on the prop valve. Cleaning the prop valve plug pins and giving them a gentle squeeze to ensure a good contact cures a lot of these problems.
It is caused by intermittent contact, when connection fails the prop starts to feather, when connction is re-established it returns to normal operation. with a loose pin or chaffed wire this shows up as a surging as the prop changes pitch. If it is ignored the result is the prop will eventually feather and stop the engine.
TAE did have a slightly dodgy prop valve supplied by a subcontractor a while back but these should all have been changed out by now.
If the engineers make sure the harness cannot chaffe and the pilots operate it within the parameters of the FM then we have few problems.
And yes the back up batteries are a back up, back up for pilots who fly with a flat battery. You would need to loose alternators and the main battery before the back up system was required.