What do you do to save the state of the diagram? Presumably you save the Diagram.model’s state somehow. Does that include the values for Diagram.position and Diagram.scale?
If you are calling Model.toJson, you could first save copies of those values in the Model.modelData object. Then after calling Model.fromJson but before setting Diagram.model, you should set Diagram.initialPosition and Diagram.initialScale to those two loaded values. That way when you set the Diagram.model the values for position and scale will eventually get those initial values.
For example, in https://github.com/NorthwoodsSoftware/GoJS/blob/4f7cd6e423df0fd15c50696516371c33c7e08b90/extensionsJSM/SnapLinkReshaping.html, look at the save...
and load...
functions.