if none of the files were handwritten, they probably came from something

Yep, I thought about Flatpak, but no, those are actually located in /var/lib/flatpak/exports/share/applications.

Turns out the files in ~/.local/share/applications were generated when I'd use the Edit Application GUI for adding environment variables to apps.

So, I didn't loose any app, I just had to wait for them to reappear and then reapply the environment variables.

doesn’t cp error when trying to copy folders without the recursive flag?

Yeah it actually did, but I didn't think anything of it and just added the flag without thinking 😅

(Because I already forget it most of the time when I do intend to copy directories so I took the habit to mechanically press Home then Ctrl-Right then space dash r...)