Disappearing tax return

We have received a late filing penalty notice for a client whose return we filed on 26 January (we have a receipt).  I have checked the client record on the HMRC website and the return does not appear to be there.

On telephoning the agent hotline I was told that the return had recently been 'unlogged' by HMRC because another agent had in error filed a return using the same UTR number for a different taxpayer, thereby overwriting our client's return.  The matter is now apparently with the Logging and Capturing Team to sort out and they are meant to be writing to us about it.

Surely it cannot be possible to overwrite a third party tax return simply by making a transposition error in a UTR number - there must be some sort of sanity check in the HMRC system, surely the return must at least contain UTR and NI numbers relating to the same person !!

I'm not at all sure that our software will allow us to re-file the return and am reluctant to do that anyway as that will now generate a notice for daily penalties on top of the £100.

Has anyone else had the same problem?  and if so did HMRC actually manage to resolve it satisfactorily?