One solution I can see would be to merge automatically the CSV from HikaShop and the CSV from your database. There are tools for that you can find online:
	www.google.com/search?ix=seb&sourceid=ch...e=UTF-8&q=csv+merger
Another solution would be for you to try to remove the code
if(empty($product->product_type)){
			if(empty($product->product_parent_id)){
				$product->product_type='main';
			}else{
				if(!empty($product->product_parent_id) && !empty($product->product_code) && $product->product_parent_id == $product->product_code){
					$app =& JFactory::getApplication();
					$app->enqueueMessage('The product '.$product->product_code.' has the same value in the product_parent_id and product_code fields which is not possible ( a main product cannot be a variant at the same time ). This product has been considered as a main product by HikaShop and has been imported as such.');
					$product->product_type='main';
					$product->product_parent_id=0;
				}else{
					$product->product_type='variant';
				}
			}
		}else{
			if(!in_array($product->product_type,array('main','variant'))){
				$product->product_type = 'main';
			}
		}
		if($product->product_type=='main'){
			if(!empty($product->product_parent_id)){
				$app =& JFactory::getApplication();
				$app->enqueueMessage('The product '.@$product->product_code.' should have an empty value instead of the value '.$product->product_parent_id.' in the field product_parent_id as it is a main product (not a variant) and thus doesn\'t have any parent.','error');
			}
		}and change the code :
$this->_insertOneTypeOfProducts($products,'main');
by:
$this->_insertOneTypeOfProducts($products,'');
in the file administrator/components/com_hikashop/helpers/import.php
That should avoid the problem.