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With apply "opacity", Sort Objects compared each object's opacity with the value it gets as a percentage, within 1e-6. An evenly stepped value can differ from a mark's percentage by more than that while it rounds to the same stored opacity: marks at 30%, 65% and 100% sorted by x with distribute on keep their opacities, yet the 65% mark counted as changed. The sort then made an undo step and replaced the opacity the graph stores for the series (30%) with 65%. The sort now compares each object's stored opacity with the opacity it is given, as stored, both to skip a run that changes nothing and to pick the marks whose opacity the graph keeps.