Hi Leigh,
as you work for a company that sells a Express ECO mod by themselves, you should no about the leaks in Innovator change management :). .
Especially the traceability task is solved much better by other PLM vendors.
I think you use both of the Actions the correct way. But both Renumber and Supersede do not contain a lot of additional functionality. As far as I know this two actions, you have to take care for the BOM replacements by yourself. But maybe you can use the edit relationship action within your ECO?
From my POV I wouldn´t like an automatic replacement of superseded/renumbered Parts in the BOM. From my POV it´s dangerous. Released BOM data is used in various places (ERP, MPP, etc.). You have to take for all this data.
Supersede should mainly influence new created BOMs ("do not use old stuff"), while old BOMs may not have to reference to the new Part. I prefer Alternates and Substitutes to highlight these kind of changes. You can automate this task by adding the necessary functions in the transition handlers by yourself.
Angela