As far as I can tell, this isn’t possible in Hype. For a workaround, I can animate in a duplicate polygon with the new border color. Just wondering if there’s a slicker way than that, since I have about 100 polygons I need to do this for. 
the bordercolor animates fine …bordercolor.hype.zip (13.1 KB)
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Excellent, thanks! Didn’t know that polygons used stroke in place of border.