Removing Link data from the graph

First, as with any transactional system, you should not be performing transactions inside loops like that.

Second, why don’t you remove the Links from the Diagram instead of removing the link data from the Model?

  var node = . . .
  myDiagram.startTransaction("Deleted Links");
  myDiagram.removeParts(node.findLinksConnected());
  myDiagram.commitTransaction("Deleted Links");

Or, if you don’t mind changing the current selection:

  var node = ...
  myDiagram.selectCollection(node.findLinksConnected());
  myDiagram.commandHandler.deleteSelection();

(Commands and tools execute their own transactions.)