Store Commander's CSV import tool allows you to create and update your products in bulk.
It is however not possible to delete products from your store using the import process.
The workaround is to move the products you wish to delete into a hidden category using the import tool.
Once the import process is complete, you can then simply drag/drop this hidden category into the SC Recycle Bin, which will also delete the products contained.
You will find detailed instructions on how to move products into a new category in this article.