Sorry, but I have no control over how the mod portal replaces files. I guess it just deletes the old folder and downloads the new one. There are some talks of properly supporting mods with settings, but I don't think those are coming anytime soon.
Trying check recycling/trash bin, or (in Windows) try right-clicking the mods folder > Properties > Previous Versions, to see if there is an automatic backup.
I guess I'll add a warning in the description, but that's the most I can do for something like this.
