Thanks so much everyone, I added a line to the .bat file based on a private message. I then ran this file again and it showed me what the problem was.
It was a MacBook/Parallels folder conflict.
So I moved my patch folder to a new directory in the Windows C: drive, instead of my usual C: drive, reran the .bat file and the patches ran, and I now have succeeded in adding them to my Kobo.
Thanks to all who helped! I will definitely find this easy to do in future.
Now - can I change the font used in the book header/footer?
I didn't like the capital letters, and now I don't like the sans serif font, especially as I always read using a serif font.