My first guess is one cylinder is firing intermittently. Perhaps a broken wire.
If it happens again; pull over but don't try to "fix" it by revving and shifting etc. Instead; try to keep it running a few minutes then see if one header is hotter than the other. If one is hotter than the other then you know one cylinder isn't firing.
Now having said that; it's safest and recommended you get it fixed before you hurl your mortal body into the arms of traffic! It could be fatal if for instance you were making a left turn between oncoming traffic! As for the shift into neutral; I'm betting it wasn't fully engaged so it kicked out of gear when the power changed or you didn't realize your foot tickled the shifter when you reacted to the change in power.
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The Smart Money: #1 - ATGATT, #2 - Training (machine skills and survival skills), #3 - The bike; whatever floats yer boat with the money you have left over
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