The permission issue is expected, given that anything under /usr requires root privileges. I think what happened here is that when you used Kate there was a file association made to continue using it for this file extension.
First, take a look at this thread to know how to navigate using the file explorer and be able to edit files that require privileges.
Then, navigate to the .desktop file you created. Right click -> Properties -> Open With -> Reset. This should remove any existing file associations for this extension and should launch shortcuts normally.