Solution
user_instance.books.remove(book_instance)
db.session.commit()
def remove(book_id):
# get the user
user = db.session.query(User).filter_by(email=session['email']).first()
# Find the book by its id
book_rm = Book.query.get(book_id)
user.books.remove(book_rm)
db.session.commit()