Hi,
You could have avoided that issue by adding your custom CSS in your template instead of adding it in HikaShop CSS file. That way, you would always use the default CSS of HikaShop and then have your CSS on top of HikaShop's.
But then, you can also have your changes not working anymore after an update because the default CSS has changed, especially with a big update like the 3.0.0
The best is to test the updates on a copy of your website, and fix the CSS there before applying the update to the live website.