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I was able to reproduced a problem on the Visual Report when using filter on the chart.
Actually, the exclude filter for the answers do take effect... it is just that the Chart color doesn't reflect it. The chart color is NOT updated while in the Visual Report creator.
Option #3 chart should be the color sky blue..
BUT in the live report, the correct chart color are applied appropriately.
In the Visual Report creator, to be able to see the correct updated graph color, you need to exit the report creator and then reload.
Let us know if this works for you or not.
I will also submit a bug ticket to our higher team support to address that minimal glitch on chart color.
We will let you know here once we have status update available.