To put this in context, the IPA annual report was published on 20 July, and covers 244 projects of which about 20 involve rail (inludes MML, East Coast Digital, E-W Rail etc, as well as HS2).
The HS2 entries are on p54 of this:
The entries simply show the project status colour coding, and a short description of the project, without any analysis.
There is no discussion of HS2 elsewhere in the document.
On p40 at the head of the listings of project status is a generic paragraph on why a project is coded green, amber, red etc.
This is the paragraph on Red projects:
All the BBC has done is to repeat these paragraphs for red and amber, as though they refer specifically to HS2.
The report is not an analytical assessment of the HS2 projects (though we might well agree with the status they have given).
The BBC report then goes into the well-known budget and timescale issues from HS2's reports.
So I don't think the IPA report presents anything new, any more than the reports of the various Parliamentary committees do.
The IPA is a Cabinet Office agency advising the PM.
It's possible the PM will react to the advice being given, but then he has 200-odd other projects to worry about, many also flashing Red in the IPA report.