Hi,
It's probably that you're missing some data in the CSV file preventing HikaShop from knowing that the elements that you're adding are variants and not main products and thus when it updates their information, it removes the link between the variant and the main product and the variant becomes itself a main product.
So I would first recommend to check the product_type and product_parent_id columns of your CSV, the characteristic column of your CSV and fact that you have the main product entry on your CSV before the variants.
Remember that the import system is to import new data, not to update the existing data.
If for example you just want to update the quantities of the products/variants with just the product_id and the product_quantity columns in your CSV, then I would recommend instead to create a mass action with a filter "CSV products". This wil really update the products/variants data without other alteration.