Hey Steve

This is what I have modified my code to currently but it had no effect, I figured that the variant is created when the product option is created, the problem is the options have been created and made to be shared via code and populates the product options just fine but I am unable to deselect the colours I don't want variants for for each product and that seems to be controlled by the "Include choice" flag

                //If doesnt exist create product
                if (existingProduct == null)
                {
                    merchelloProduct = this.MerchelloServices.ProductService.CreateProductWithKey(product.ProductName, product.ProductCode, product.PriceExclVat.Value);
                    merchelloProduct.Available = true;
                }
                else
                {
                    merchelloProduct = existingProduct;
                }

                if (merchelloProduct.Sku == product.ProductCode)
                {
                    var productOptions = currentOptions.Items.Where(x => x.Name == "Colour").FirstOrDefault();

                    merchelloProduct.ProductOptions = new ProductOptionCollection { productOptions };

                    merchelloProduct.ProductOptions.Where(x => x.Name == "Colour").FirstOrDefault()
                                    .Choices.Where(x => x.Sku == product.ColourSku).FirstOrDefault().IsDefaultChoice = true;
                }