I think the whole idea of having desktop-files is absurd.
That aside, i don’t know what changed when. Seeing as how i don’t worry about desktop files. All the stuff i use is set up as icons in panels, or the infrequently used stuff like calculator is available in the mate app-menu.
[Take the idea of having icons in panels, that you can actually modify to point at real commands with real parameters, and add another “panel” that represents all the screen real-estate not already covered by the top/bottom/left/right panels, and the whole issue of having or editing desktop-files becomes moot.]
Anyway you still want to edit the things. For that, the only help i can offer is my nautilusExtension utillity, which i’ve posted about before. If you can get caja or nautilus to select the file, it’ll let you edit it readonly or readwrite and if necessary it’ll relaunch itself as root so you can do the edit you want to do. Unfortunately, even though it’s one self-contained file, it relies on a working PHP installation (not necessarily for Apache, just for commands), so that’s something i can’t help with. PHP installation is worse than Apache because it presumes Apache and then adds about a thousand more semi-documented configuration variables that do who-knows-what. It probably requires other things i’ve forgotten about (like zenity for dialogs, nedit for editing), and the menu layout is cryptic and undocumented, since PHP being such a mortal PITA there was never any expectation others would use it.
But, it’s non-hostile (even though maybe stupid) and it’ll do many nice things that the caja lames didn’t think to include… like putting the name of the goddamn file in the clipboard so you can trot over to the paleolithic command terminal and ctl/alt/v it into a command.
IOW i can’t do a thing to help, but i do feel your pain. fwiw.
[edit: sorry to have seemed so… rancid maybe is the word, but when i got into computing long ago i really had high hopes for it, and other than apologizing for my tone, i’m not changing a thing.]