Either use the flowchart's CreateArrow method or use this Arrow constructor:

public Arrow(FlowChart parent, Node src, PointF dest)

to create the arrow and the add it to the flowchart with the Add method:

Arrow a = fc.CreateArrow(src, dst);

- or -

Arrow a = new Arrow(fc, src, dst);
fc.Add(a);

These methods add the new arrows to several collections - to fc.Objects, fc.Arrows, src.OutgoingArrows and dst.IncomingArrows.So use the methods instead of adding arrows manually to all the collections.