A capacitor, IMHO, would only help to bring the time an ECU can sustain a power transient, from 1.7 to 50 ms. I don't know what the switching time for a relay is, but this sounds about right for that. But 50 ms would not be enough to sustain a too-low bus voltage due to gear retraction - unless the DA-42 has some of the fastest retracting gear in the industry.
Backup battery sounds like the way to go.