Hey Ruchika,
Well, you will have some work in this case. The main goal of CMigrator was to migrate the data, after that you should be working on the migrated data. In your case you are looking for a sync tool and CMigrator is not that. However we have an option that could help you. In the migration settings we have an option "clean migration". If you set it to no, then we won't wipe out the current content on the site. If we find that you already have a category with the name "something", then we will add the new category as "something - cmigrator copy1". In this category we will add all articles from the site. So in your case if you do that you will have the data and you would need to manually move the new articles to the old category. And after that you can delete the new categories.
Regards,
Daniel
P.S. As usual make a backup before doing the migration. Also this kind of migration is slow. We need to check for each item if it exist, if it doesn't then we add it. If the item exist we add it with a new title "old title + cmigrator copy 1, 2,3,4 etc"