Hi,
When you set that option to "use canonical URL and generate if missing" and that the canonical URL field of the product/category are empty, then, the first time a module or menu has to display the link to that product/category, the system will fall back in "no, generate it" and take that URL and put it in the canonical URL field of the product/category. The next time HikaShop has to display a link to that product/category it will be able to directly use the canonical URL.
So if you configured different menus and modules to access the products, with that option deactivated, you can see that different links are used. Among them, one of them is that link that HikaShop used as canonical URL.
If that link is not to your liking, then you need to enter the link you want instead.
The best here is that when you products/categories canonical URL field is empty and you activate that option, you can directly browse your website to the different products listings using the menu/module which generates normally the links you want as canonical URLs. That way, HikaShop will be able to pickup these links as canonical URLs instead of other links.
And if you want to clear all the canonical URLs of your categories/products, you can use the mass actions system for that:
www.hikashop.com/support/documentation/167-massaction-form.html
www.hikashop.com/forum/content-creation/...s-from-hikashop.html