To make my question/info complete, see the photo what Hakchi does when I add a zip of Metal Slug to it (got the same roms from several sources now, all react the same with this pop-up, so just the Neo Geo games/zips)
View attachment 102288
Well. I guess haxchi tries to zip just the one file because its set up to add one file roms. What you could try to do is let it add one of the files, then go to the game folder in the games_snes, add the zipped rom to it, and just rename it to the same as the one thats in there.
Then again that probably wont work. Depends if its looking for the specific .7z file.
Maybe you could add the whole zipped rom into the 7z and delete the odd file.