If the visibility of the div containing the graph gets set to hidden almost everything disappears as expected except the second y-axis and the legend items.
To repoduce go to:
http://c3js.org/samples/axes_y2.html
Then select a parent div or the body and set it's visibility to hidden.
*also seems to have the same problem in IE
*In firefox the other axes also stay visible.
*when you turn the visibility back on the axes that where correctly hidden will stay hidden.
*seems to have something to do with clip-paths. The 2nd y-axis and the legend items don't have a clip path. If I give the 2nd y-axis the same clip-path as the 1st axis it is hidden correctly when I set the container to hidden.