They might struggle a bit; I'd go for at least 100A of constant discharge ability. That's a sweet conversion though! Very clean, and great layout. Good job.
They aren't perfect, but 6S won't draw as much current anyway (if you are gearing for the same speed). Only thing is, hardcased 3S lipos that are high capacity aren't that common. I think LRP do one, but I don't like their cells. Could just be me though...
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This has made a lot of people very angry and has been widely regarded as a bad move.