I had the same issue this morning - I had to remove and the re-add the extensions for HIPS to get round the issue. Once logged into your current EPO go to menu, software, extensions and remove HIPS. Epo 5.3.1 will then allow you to install. Once it's installed you can then go back to extensions and re-add it back in, then check it in using the software manager. You just need to have it downloaded from the mcafee website using your grant number.
Ding, ding! Winner. Thank you! I removed the the HiPS extensions (did not reboot after), and then ran the 5.3.1 upgrade without issue.
I'm having trouble installing the same (current) HiPS extensions now. It thinks they're already installed, but they don't display in the extensions page. I'll figure that as I go, but for now, the upgrade issue is resolved.