I need to enable iCloud feature in my current app which has an existing version in AppStore.
What I can see from enabling the iCloud,
Is making my existing provisioning Invalid,
The Invalid is making me worried, Will it effect my existing app in AppStore.
Note* I have tried the above in demo project.
In short No, it won't affect any of your existing apps on the App Store.
Modifying/Deleting any App-ID, Provisioning Profile or Certificate has no effect what so ever once you have submitted the App.
However, you will have to use the new configuration for your next release.