The Capture One subfolder, containing among other things the jpg.cos files, are created whenever you view a folder with images from within Capture One, including the output folder. If you haven't made any adjustments to your files, the .cos files will just contain the default settings.
My guess is that you browsed to the output folder using Capture One and then creating the extra files. If you haven't made any adjustments to the files, you can safely delete the Capture One sub folder.
This is correct.