Smoke your cigar as you usually would. When you're through, put it out on your canker sore. Canker sore problem solved.
Realistically, I'd recommend holding off smoking until it goes away. I doubt you're suffering long term negative effects, but if the smoke (or even the act of drawing on the cigar) is irritating the sore, it will probably take longer to heal.*
*I'm no Doctor, but I play one on TV
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