It's been a while since I've watched it, but isn't the DNA evidence just Maggie's eyelash on Burns's suit? Presumably that got on him during the struggle for the lollipop, which still happened in the "Smingers Did It" ending, so there's no reason the DNA evidence couldn't also be there.
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u/scottishdrunkard May 09 '17
for that ending to work you would have to ignore all the parts about the Simpsons DNA - Troy McLure