With a bit of persistence in searching, I have found the answer. It is actually in the object browser in Project 2013, but I didn't see it in the Project Model on MSDN.
So, here is a simple toggle macro for the original question and for my question (but same solution really).
I know there is a way to write a toggle more succinctly, but apart from the fact that I cannot remember how, this also shows the logic better.
Hope this helps!
Nic.
Sub ToggleAutoLink()
Dim ap As Project
Set ap = ActiveProject
If ap.AutoLinkTasks = True Then
ap.AutoLinkTasks = False
Else
ap.AutoLinkTasks = True
End If
End Sub
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Sub ToggleSplitInProgess()
Dim ap As Project
Set ap = ActiveProject
If ap.AutoSplitTasks = True Then
ap.AutoSplitTasks = False
Else
ap.AutoSplitTasks = True
End If
End Sub