We at this point--and that's me as a citizen of the country and you as parliamentarians--do not know how the “not” got there. What we do know is that the minister did not repudiate that “not”. I don't think there is any more issue than that.
The letter was presented, purported as being a letter supported by the intentions of three officials--two in the department, and the minister--and it turns out that the intention of the letter as presented supported only the views of one of those three. I think that is all that needs to be said on that.