If you start the PI with a filter (a System Pref in the PI tool), the START quantity is recorded ONLY for items in that filter. The danger is that if the customer wants to update at the end for items not in the original filter, the START QTY defaults to 0 and thus the update would be innaccurate.

The morale of the story is if the client is using the option to USE FILTER TO START, they need to start with the correct filter. If the original filter is not correct, the PI needs to be restarted.