Hi Pablo,
What ever the qty you have entered for as a scrap in CO11N, that stock qty will be vanished. It's only for information/reporting purpose. Since you have confirmed the production order by operation wise in CO11N. What ever the materials(Components) which are required to manufacture the assembly in BOM, will be consumed ( mvmt 261) during operation confirmation. If you know the scrap qty of your assembly or the qty o scrap is fixed, then create a material for scrap and add it to assembly's BOM with negative(-) value. So, when you do production order confirmation(CO11N), system automatically will post 551 movement for scrap material to inventory.
Thanks