Although the manual instructs that the external power should be disconnected after the first is started it does not warn that the second engine should not also be started the same way. It does not warn that you must wait for the flat battery to recharge sufficiently to a minimum level before takeoff in order to be relied upon later.
I believe you are incorrect.
I’d have to dig into my pile of old manuals but the DA-42 1.7 did come with a warning not to start both engines with external power.
I believe also the Battery Master switch was never turned on so the electrical system was running off the generators without the benefit of the buffering function of a battery and the ECU’s “blinked” as a result of the brief fluctuation as the electric hydraulic pump kicked in.
The backup batteries installed as a result of that pilot induced incident did not have to be rechargeable as per EASA certification.
The original Thielert 1.7L was and is still my favorite engine for that airplane.