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The problem was that rule-based renderer allowed cloned rules to have the same unique rule key. That in turn created the confusion with checkboxes in legend. Now rules always have new rule key when cloned. The only exception is when the whole renderer is cloned - in such case we preserve their rule keys, so that other components (legend / visibility presets) can still keep using the original rule keys. Projects where this problem appears need to be fixed - the easiest way is to select all rules, copy&paste them and remove the previous rules.