More than a few times, I’ve applied a filter (smoothing, etc) to a segment that I had accidentally selected but was not visible, and then thought that nothing had happened. What about a warning box saying that the filter to be applied is about to operate on a non-visible segment? (Happy to look into adding this if you think it would be useful.)
I agree, we could put a small warning icon (similar to the rotated slice warning) next to the “Apply” button that could help users to avoid this. The icon could have a tooltip that explains that selected segment is not visible and maybe it could be a button (clicking that would make the segment visible).