After setting the LayerSpacing property the diagram quickly responds.
However, if the diagram layout (LayeredDigraphLayout) has horizontal orientation (i.e. layoutForFlowDiagram.Direction == 0.0) and the links have LinkRouting.AvoidsNodes, then some of the links disappear. I think they are still in the model somewhere but are not displayed.
The links are some (but not necessarily all) those which are between Next Level Groups. Links between Top Level Groups remain intact.
I thought that if, once the diagram layout has finished respacing the layers, I could catch an event, then in the handler I could find all such disappeared links and cause them to redisplay.
A similar situation existed when Top Level Groups are dragged, but I fixed it by adding a handler for MyJobsFlowDiagram.SelectionMoved.
With normal flow link routing there are connections from JOBD.AB to JOBI.AA and JOBD.AC to JOBIAB