Hi,
The problem is that you put the popup button in the description and that the description is refreshed when you select another variant as you can have different descriptions for different variants. And your popup button doesn't handle the reinit of the popup modal system for the new button.
In your button, you should actually have an onclick attribute which would call the fromElement function of the modal JS library to reload the button when you click on it and that would work.
But as a quick fix, you can simply remove the code:
<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>
of the file "show" of the view "product" via the menu Display->Views and that will remove the refresh of the description on the product page when you select a variant.