Ok, since it was a live website I had no other choice then to restore a backup using an older version of VM 2.
Unfortunately, I now experience the problem again with another website. I have made a copy of
this website and placed it here to work on it. After updating Joomla, extensions (JCE Editor, XMap, etc) and Virtuemart, exactly the same error comes up when you place something in the cart "Error the quantity of the product for calculation is 0, please notify the shopowner, the product id 0".
The new version of the website where the error shows up can be seen
here.
This is really driving me mad, any help is greatly appreciated!