Kevin,
When you only have the javaBE.ini that changed, you can have this application zip file loaded again into the Agentry editor (assumption newer SMP 3.0 SDK than the Service Manager 4.2 exe files zip file).
During publishing, there is a blank area in the middle of the window. You can right click on this to create files, folders and add files. You also have a generic setup that you can do to save your settings when publishing. The goal is to zip all the needed files again by publishing a production.
What I did with a customer is I just unzip the published files that came from the executable files into another folder. I modified the file I needed to modify (in your case the javaBe.ini) and in the editor I load it up in a new workspace. I then will point to my development folder. I will then publish as production. In this middle area you right click and add the needed files to complete the zip file (in my example, I recreated all the folders and added all the files in this middle section of the production editor publish).
You will point to a blank folder to be a destination of your publish files (you may be instructed to reference your development server too). In theory, you will have a new zip file (with all the needed files to complete the mobility project) and this will work with the cockpit. Assumption is the cockpit is the same version of your editor.
Hope this works.
Regards,
Mark Pe
SAP Platinum Support Engineer