Hi,
1. There is no "recommended" choice. It depends on what you want to do.
2. Once a canonical URL is set in a product, if you activate the "Force canonical URLs on listings" setting, that URL will be used by HikaShop. If you change something on your website which renders that canonical URL invalid, then the URL used on the listings will be invalid until either you empty the canonical URL or fix it.
3. Even if you deactivate the "Force canonical URLs on listings" setting, you need to have valid canonical URLs or it will hamper your SEO efforts. It's better to not have a canonical URL, than having a wrong one.
So regarding "solutions", I have many but it depends what you want...
You could fix the canonical URLs of the products that have a wrong one manually
You could empty the canonical URLs
You could just turn off the "Force canonical URLs on listings" setting, but it will be less good for your SEO