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In case where an edge has been deleted and one of its extremities has moved and the other extremity has been deleted, the computed phantom related to the edge is drawn from the moved node to (0,0) location. It should end to the phantom related to the deleted node. In this context, an edit part is created for the edge phantom (in order to compute the line to draw to the new location for its extremity). The source edit part is retrieved from the GMF node but there is no target edit part to the deleted node (it does not exist anymore, replaced by a phantom (just a GEF figure)). So, the target extremity of the edge is located to (0,0) by default. A GEF edit part has to be created. It will build an invisible figure with the same bounds of the target phantom and it will be attached to the edge phantom edit part (as target) in order that the edge be connect to the node phantom.
Created attachment 234903 [details] data set
I can't reproduce. This issue seems to be already fixed