By going to the Kobo website and deleting the books.
The
My Library link has three distinct areas;
I'm Reading,
Purchased and
Trash.
When you go to Reading you can check the box besides each book and then hit the Delete button. Books will be removed from the list and will only remain in Trash. Not to worry, Trash is a misnomer; items stay there until permanently removed by you.
When a book is in Trash it will not sync via either Desktop or WiFi.
ALso, within Kobo Desktop, when your device is connected a little symbol will appear besides each book in your library that will allow you to say sync / don't sync on each book.