Also, to bg6579, you suggest later on writing to them to ask them to follow the correct procedure. Could you elaborate on what you think that would be based on the facts as stated?
An assessment doesn't change a tax return. As previously stated, your tax return and self-assessment (they go hand in hand) are final and cannot be amended by anyone. An assessment creates a tax charge that is in addition to the amount self-assessed.
I really do not know the correct answer to your question. I suggested earlier that HMRC could raise an assessment without giving relief for the losses brought forward. That would leave you to appeal the assessment and then, if PPR is not due and a gain does in fact arise, use your losses to reduce the gain. However, I am not wholly persuaded that would be correct.
As I suggested before, I'd simply tell HMRC that you are able to amend the return because the time limit for doing so has passed (s9ZA TMA 1970) meaning any such amendment would be invalid, and they are unable to amend the return under s28A because they have not given notice of enquiry under s9A. Ask them to tell you what they consider the correct procedure to be. It puts the ball firmly in their court to set out the correct position as they see it.