Hi,
When debugging your website, I processed a massaction before my commit was done, so I lost the settings, please give me the url of the csv file to set in the path field.
The issue seems to be coming from the fact that if no products are found in the database, so all the products are loaded.
This will be fast to fix.
Regarding the "lost products" issue you have, the listing don't see them because they don't have categories, so the system just can't list them, the mass action see them because it is only based on the product ids, no checks are done on the categories.
But, to retrieve these products, you just have to click on the "Check database" button in the toolbar of the HikaShop configuration page.