A late refusal notice is arguably invalid BUT if it is not challenged in a timely fashion it can arguably acquire force in time.
(I can't recall any prior approval cases, but there is a long line of other cases re the validity of various other planning decisions which suggest this could happen.)
Obviously from an LPA point of view the correct procedure is to avoid this situation....
From a homeowner/developer's point of view I would suggest first is to query the dates and documents with the Council involved. Perhaps the application was not received when you think, or perhaps not all of the information was submitted at first, perhaps someone agreed additional time. If it still appears that the refusal was out of time then you might consider an appeal as the next step. I would be extremely cautious about just starting work on the basis that the notice is arguably invalid without questioning/challenging the notice and settling this.
