Aldo, I've already explained that the changes are tracked in the schedule lines (VBEP), not in the line item (VBAP). Do you understand the difference between them?
In your case when the quantity is changed, the schedule lines are deleted and I'm guessing new lines are created. To find why this is happening in your system, please speak to a local SD expert. This could be either something to do with ATP or a user exit, there is really no way for SCN members to know. It is a standard functionality though to delete schedule lines and recreate them instead of changing under certain conditions - I've seen this happen in other systems too.
Not sure why exactly this is a problem though - is there some kind of a legal requirement? What are you trying to achieve?