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.
No trigger is given on a stock change from your ERP to update your stock. If the API of your ERP makes this possible in your API to send a mutation date of your stock, it will of course be triggered to be updated by the sync.