Thank you for the link to the updated v3.1 manual.
The older v3.1 of the manual I have that didn't have more than 151 pages and has a date of 1.6.12 with this final portion in its description:
"... updated App. A and C, and expanded App. B and E, also explaining the floating point formats; added appendices covering the emulator and troubleshooting"
While the newer v3.1 of the manual is dated 27.7.12 and has 180 pages with this final portion in its description:
"... abandoned the internal expert’s catalog; updated and rearranged large parts of the introductory text and the appendices, also explaining the floating point formats, the emulator, troubleshooting, and corresponding operations of HP-42S."
I'm not sure why the manual with these extensive amount of changes didn't warrant a new suffix number to differentiate it from the one downloaded earlier. Yet, maybe, the version number has more to do with the emulator than it does to the owner's manual.