[findsolution]

Thanks all for your valuable inputs. The issue has been resolved and we have successfully deleted the application and software configuration from the Admin console.

We had assigned this config to 2 users, and for both the users the software configuration tab was showing that there are no configurations assigned to these user.

I spoke to both these users and found that the application had got successfully deleted from their devices also. With permission from these 2 users I deleted their BES accounts and then I could delete the APP as well as the config. The users devices will configured again.

Still no clue as to what could have happened, but the issue is resolved...