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When using dynamic labels with Simple Line Callouts, labels erratically appear or disappear.
Though the problem may appear as you are setting or clearing a reference scale or while zooming in or out on the map, it has nothing to do with either. The problem is that the Simple Line Callout is not very reliable when used with dynamic labels.
Use a Line Callout, but adjust the gap distance as needed and turn off the Accent Bar and Border options when creating dynamic labels.