I guess, as it happens always, these proxy elements are located in the same package of the diagram they are created in. Every time you create a new element (a new row in t_object table) in a diagram, its parent package is the same as the diagram parent package.
So, my suggestion is: create a locked package (in order to avoid user deletion), and via your automation relocate the proxy elements as children of this package. If you don't delete the package, the elements will remain in the model.