Are you using GML commander?
If so, then the stop button should stop the execution of the program, HOWEVER, if the CPU is very busy, it may take two or three tries in quick succession to actually get the thing stoppped.
The bad news, is that you cannot upload a GML diagram from the controller. When an S-Class or 1394 controller is downloaded, GML software coverts the diagram to a script file and that is what gets downloaded, along with the setups and tuning values.
So, you can only upload a script file, the setup values, and the variables (my terminology may be inexact, it has been several years since I used GML).
Now, it is possible, but very time consuming to recreate a GML diagram that would result in the same script that was downloaded, but the level of difficulty in doing that depends mainly on how complex a program you have.
For the purpose of an emergency backup, the script file, along with the other two files containing all the tuning data and variables, can be used, it just can't be modified very readily using GML.
I hope this helps, and let us know what your controller firmware revision level and software versions are if you have further questions.
Paul