Haage & Partner licensed or aquired code from third parties which is part of the AmigaOS 3.5/3.9 update. They also created code in house which is part of AmigaOS 3.5/3.9, and they also paid developers to create code for it. The company still owns this software and, to the best of my knowledge, has not licensed or sold it yet.
None of this specific code owned by Haage & Partner is tangled up with the Amiga International-licensed AmigaOS 3.1 code. Even if Haage & Partner wanted to, they could not "bake" a fully legally sanctioned AmigaOS 3.9 out of their properties and AmigaOS 3.1.
Yes, it sounds weird, because it is. This is the Amiga business, after all 
Ah, that makes perfect sense. So until there's a clear owner of OS3.1 and the IP associated with it, Haage & Partner can't release and distribute a full-blown update of OS3.9. I'm not sure that this issue will ever get lined out. There are just too many vultures fighting over the dead carcass of OS3.1 and they fail to realize that there isn't a significant amount of money to be made even if they gained said rights. Even with the Vampire's popularity I would guess that there would be fewer than 100 buyers of a Vampire specific release of OS3.1. Most Vampire owners already own a copy of OS3.1 or 3.9 and they're quite happy to just patch their existing copies as needed.
Dreaming of an Amiga revival where Vampires are being sold in the tens of thousands bundled with copies of OS3.1 licensed from Hyperion borders on the absurd, but delusional business plans run rampant in this hobby that encompasses dead hardware and dead operating systems....