When converting pencil to brush strokes i can flatten the line art but when keeping the drawing in pencil it appears that the flatten tool is not working , I did also try the remove extra strokes function after flattening but it still does not work.
Pencil lines of the same colour can be flattened together. If there are several colours used for the line, multiple line sets will be created. Pencil line size does not affect the flatten.
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There must be more going on with your artwork. I can draw a pencil line and have the option to flatten it in Animate and Animate Pro. Try creating a test project file. Just draw a circle with the Pencil Tool and see what your options are.