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In my models, I sometimes add notes from the general Palette (by using the yellow note symbol), and attach them to elements (including to edges). I have noticed that upon reconnection of element-based edges (changing source or target of the edge), the attached note becomes detached (so that the note remains, but is no longer connected to the edge). I suspect this is a bug that should be addressed. This bug was reproduced by Steve Monnier of Obeo
Indeed, I think that after reconnection the refresh creates a new DEdge (or at leat a new GMF Edge) and the note attachment is not reconnect to it as it is not the same graphical model element.