I submitted a set of accounts using Web Filing last night just before the deadline.
A box came up showing the accounts had been transferred but I didn't get a reference number and I didn't get an email.
I phoned Companies House this morning and it seems the standard response is "They weren't submitted. If they had been submitted you would have got a reference number."
I pointed out that I saw the transfer taking place in the box on the screen and the problem must have arisen after the transfer and before the submission number was issued.
A few months ago I had a similar problem and my wife went to the client and got the accounts signed and she dropped them off at Companies House before the deadline.
Companies House make out their software is never at fault.
I'm chasing clients as soon as they should have the information this year but that's not possible when new clients come to you a couple of weeks before the accounts deadline.