Route planning aside, it sounds like your problem was that a short circuit in the ECU emptied the battery, rather than a flat battery damaging the ECU.
So all the battery testing was a bit of a moot point.
The people who suggested a battery maintainer wre suggesting something that would have left all your batteries flat (and maybe damaged). After all, a parasitic drain that empties a starter battery in x hours or days will empty the lot in 4x hours or days.
The moral is that you should find the cause of a problem before fixing it, and before blaming one component, whether your innocent battery or your blameless charger.
Glad it is sorted, though!
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