Hi Pedro,
It is not recommended to change the quantity of the sales order to match the quantity that was delivered.
Suppose that you have a sales order (MTO) for 2000 PC of your product, the planned order will be created for 2000 PC. Now suppose that you only produce 1800 PC. For the remaining 200 PC you can define multiple options according to your business needs:
1- You can define a process where you ask your customer if he is still interested in the remaining 200 PC for a future day and then run the MPR to create a new planned order.
2- You can set a cancellation reason where you indicate the reason why the stock was not produced.
etc..
3- You can modify the sales order quantity (this is what you are doing and in my perspective it is not recommended).
I think you should go for options 1 and 2.
Kind Regards,
Mariano