Hi,
First please note that there are two import systems in HikaShop:
- The import in the Products>Import menu, which is meant to import new products primarily.
- The import filter of mass actions in System>Mass actions, which is meant to update products information.
I'll suppose that you're using the first one here. So first, I would rather recommend you use the second one for what you want to do, it's much more suitable.
Then, if you use the first import, if you set the "product_type" to "variant" and you have the id of a main product in product_id (or the code of a main product in product_code), it will actually remove the categories of that product as the system will suppose that you're importing variant. So it could be linked to that.
Also, with the first import, if you have the option "Update products information if the product_code already exists" activated, it will delete the link between the categories and the products if no category is provided in the CSV and the product is found. So make sure that is option is turned off if you don't want that to happen.