You can copy the .m files to the new folder as well and then modify the text present in the model as well as the callback function for the example to point to the new .m files.
For modifying the callback function, go to Modelling Tab -> Model Settings and update the PreLoadFcn with the new/copied file names. It is recommended to give the copied files a new name so that they are not shadowed by the .m files in the example folder. See schreenshot below:
You can see which file is being used by running the following command in the command window:
which GammaStirlingEngineParams
Similarily, you can update the text in the model by right-clicking on it and clicking "edit text". Further the hyperlink can be edited by clicking on the and using "Ctrl-K" or right-clicking it and chossing Hyperlink. Change the command to point to the .m files in the new folder. You can also specify the entire path instead of just the name.
See screenshot below:
Hope this helps!