Hi Naveen ,
Have you generated the XML using MOPZ both the times . If Mopz has been used and it had automatically calculated the files then believe there is no issue and you could go ahead releasing the system to end user
If you have manually edited the files then there could be sometimes dependency issues ( Believe the system in concern is not a production system and you have done sufficient tests in QA if it is prod )
Check whether the tools mentioned in the following link will help you
Tools to predict changes and new features in Upgrades: a brief overview
Thanks ,
Manu