Hi,
That's because the characteristic system updates dynamically the description of the product for the one of the selected variant and if you didn't enter any, it uses the main product one.
If you don't want that, you can edit the file "show" of the view "product" via the menu Display>Views and remove the code:
if(!empty($variant->product_description)) {
?>
<div id="hikashop_product_description_<?php echo $variant_name;?>" style="display:none;"><?php
echo JHTML::_('content.prepare',preg_replace('#<hr *id="system-readmore" */>#i','',$variant->product_description));
?></div>
<?php
}