Hi,
You should first open the CSV file with Excel or LibreOffice Calc and remove the columns you don't need to keep only the SKU and the quantity columns. Then, change the title of these columns to product_code and product_quantity.
Then, go in the menu System>Mass actions of HikaShop and click on the "new" button.
There, select the "product" data, and add a filter "CSV products". In it, upload the CSV file and check the "Save the products on Mass Action csv import." checkbox.
Once done, click on the "process" button at the top and it will run the import and update the quantity of the products in the CSV file.