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When adding a message to a Sequence Diagram Enterprise Architects Architect recalculates the other Messages and changes properties like SeqNo, Offsets, ... .

When working parallel on the same Sequence Diagram in different branches, adding/removing messages and merging it them with LemonTree this can  may cause unexpected results with positioning of the messages since LemonTree is a compare/merge tool and does not recalculate the diagram as EA does when adding a message to the Sequence diagram.