Thank you for that bug report. That is now fixed on our end and will be included in next release.
In the mean time, you can change the code
Code:
$query = 'INSERT IGNORE INTO '.hikashop::table('variant').' (variant_characteristic_id,variant_product_id,ordering) VALUES '.implode(',',$insert).';';
to
Code:
$query = 'REPLACE INTO '.hikashop::table('variant').' (variant_characteristic_id,variant_product_id,ordering) VALUES '.implode(',',$insert).';';
in the file adminsitrator/components/com_hikashop/classes/product.php near line 350 to fix the problem.
