We scan all products from 0 to your last product and start again. There is no filter on this, whether a product has a webshop filter or not.
So it is normal that you regularly get the error: Product 00.000.00 does not exist.
It will only update the stock of products that are in your other application.
Scanning is done every 5 min, with a maximum of 10 products in each scan. So if you have 1000 products it will take about 8 hours for all your products to be updated with the relevant stock.
This applies to all ERP systems, there is no filter in an ERP in the stock endpoint.