From a text editor, do a binding between 2 Buttons, on the layoutY property.
Launch SB.
When moving the source of the binding, the 2 Buttons move vertically together : fine.
Now if one move the other Button (the binding destination), the LayoutY value change in the inspector.
However, the binding is still active.
If one save, the binding is lost in the fxml file.

Same issue with all the properties that can be modified from the Content View (prefWidth, prefHeight, ...).
In this cases, we could warn the user a binding has been removed, and actually remove the binding (when it will be possible).