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In ArcMap, when a version is changed, the edited feature-linked annotation is moved out of the feature dataset and has a red exclamation mark beside the icon.
The sde error log records the following error:
"The featureclasses default subtype code cannot be retrieved or is invalid".
If a schema change is made to a feature-linked annotation that has an annotation classid and a default subtype, the annotation is removed from the feature dataset and has a red exclamation mark beside the icon in ArcMap when the version is changed.
Change the default subtype from a value to NULL. If an annotation feature class has one annotation class, it should not have a subtype.