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Such link cannot be created twice, meaning that if the element is already in the feature list (ex: annotated elements) the link cannot be created, but with re-orient it is possible to obtain a situation where several occurrence exists (it should be possible due to multi-diagram anyway). In such a case, destroy the link, re-orienting, or modifying the related feature in preferences should result in the destruction of all inconsistent links.
It is still possible to create inconsistencies between graphic and model in current 0.10.X version. Behavior is not specific to SysML and can be produced with a class diagram as well. Steps to reproduce - Create a comment and two classes. Add a link from the comment to each class => annotated elements list contains both classes - Now re-target one of the links to the first class => annotated elements list contains only the first class - Now undo the re-target the targeting one of the links to the 2nd class again => diagram shows two links, but annotated elements list contains only the 2nd class.