Thanks for the feedback. FYI, I posted the same issue on the Smart car forum, under the towing section, for those who are interested in the thread. ( Smart Car brakes blown using Blue Ox Patriot - Smart Car Forums
I got one very thoughtful reply, which seems to me to be closest to the mark. The poster mentioned his distrust of the Smart car "waking up" during towing- he uses wireless only for brake control of the Smart. The manual recommends switching off the Smart battery during towing (I assumed that putting the ignition key in the off position would suffice, and indeed all the various forum posts seem happy with doing just this). He also recommended charging the Patriot from the motor home, and not from any 12V power port from the Smart (I have ordered a Roadmaster 12V auxiliary power port to do just this), but now I think that switching off the Smart battery, plus powering the Patriot from the motorhome may be the answer. It is true that the manual states that the brakes can lock up at >8 miles /hr if the system is towed incorrectly, and that does seem to be what happened to us, even though the ignition was indeed off. So, if the computer wakes up- and it can because the battery is not switched off- then trouble could ensue.
Anyhoo, this is where I am at, and at least feel that there is a feasible cause, or sequence of events, that could explain the whole shebang. If any one else is flat towing a Smart car, wish us all luck!