The 3.1.4 icons are not in a new icon format. They are in GlowIcon format which is about two decades old.
AmigaOS 3.1.4 is designed as an update to 3.1, and not to 3.9, although it brings fixes, features and updates that were not present in 3.9.
Please read the FAQ completely. You are missunderstanding what AmigaOS 3.1.4 actually is.
If you want to do a merge between both you can try
http://aminet.net/misc/os/Updateto314.lha