Apple script - How is the application registered?

I wrote an Apple Script file that stops working after I change the application I am using from an actual directory to a link. This change was made to make it easier to change application versions.

How can I relink the link as an application so that the Script will run the correct file? Currently, I always get an "Unknown Application" error when running the script.

Edit: I am now starting the application manually. So it has nothing to do with running