Neil,
thanks or your reply. I am currently using the free version of this tool and am finding it generally very useful. I don't think it can actually solve this particular problem (update the source url of a registered service item with credentials stored). The Pro version likely could do it via the way you describe it, which in fairness is really a delete and recreate rather than an update.
In any case, I want to say "thanks" for your work on these tools. I think there is definitely a need for them, especially for hybrid deployments that integrate ArcGIS Server with ArcGIS Online. I really liked using them so far.
Thanks,
Tobias