Check the status of your delivery from Royal Mails website (Track & Trace). If you don't have the reference number of your Royal Mail special delivery, then call up the NCS office and
a) Ask them the Royal Mail reference number
b) Tell them why you are calling & there has been no debit from your account.
By now you should have not only got the acknowledgement from home office but also teh debit should have taken place. The only reasons this has not happened could be either because NCS has not posted, Royal mail has not delievered or home office has not started looking at your application.
If its posted & delivered, then you will have proof of delivery from Royal Mails website.
Best wishes.