4100 is a portion of the part number for an S-Class motion controller.
You should be able to communicate with it using GML commander.
You cannot upload a GML diagram. You can upload the program script, variables and setup values.
You will have to stop the program in order to do the upload.
You should go to the literature library at ab.com and search for manuals pertaining to your specific controller, and for manuals pertaining to GML commander software.
There are a lot of variations of the S-Class, and many options available for communications. Also, there have been several firmware chagnes over the years, so the release notes for your particular controller will be important to study as well.
With the exact whole part number and more information about the options and the application, I could probably offer more advice.
The ideal situation would be that you have a copy of the original GML diagram with which the machine was programmed. In that case, you could go online and upload the setups and variables, then have a complete program to download to the spare controller.
Again, I am not sure that you have an s-class. All the S-Class controllers I worked with had Allen-Bradley logos, and not Creonics. They are very similar to the Creonics Max controllers, but have a gray enclosure with a hinged door on the front.
Paul