If the engine just quits immediately, as if the ignition switch had been turned off, it is very unlikely to be a fuel problem and extremely likely to be electrical. The fact the bike will fire right back up makes it unlikely to be a temperature related breakdown of one of the electronic components, but as you said anything is possible. I would be more inclined to start with the simpler things, like the run/stop switch and wiring, the ignition switch and wiring, the ECM connector, etc.
This sort of thing is what drove many old timer's out of the automotive repair business when cars became overly complex with electronics. We all like the many things electronics can do for us, but there is still a lot to be said for the old simple systems of our youth.
Have you contacted H-D to get it on record, just in case whatever it is finally fails completely? Might be a good idea if you haven't. And who knows, maybe someone there has actually come across the same issue and could tell your dealer what to fix (yeah, I know that's pretty weak, but I wanted to offer some small measure of hope). Good Luck!
Jerry