I know this is an old thread, but I had the EXACT same problem on my XT600 3AJ, I had started my bike, it ran for a while, and all of a sudden the lights started flickering and the entire electics died. Nothing happened at all when the ignition was switched on.
In the end I discovered that the main fuse box has actually melted after overheating from a blown fuse. I cleaned up the electrics around the fuse box and replaced it with a brand new modern inline blade fuse box (20A). I also hunted down the cause of the fuse blowing and melting the fusebox which ended up being a wire that ran into my headlight unit shorting out.
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