I hope I am understanding your situation correctly. It seems you are trying to migrate from some older technology.
- I am guessing by mentioning a collider that you need a physics engine. I posted a list of Haxe physics engines here. While there is Away3D example code for MD2, I think you would have a better workflow if you use a different file format such as DAE (what I use) or 3DS or possibly FBX which is also used by Heaps3D for Haxe.
- Because Prefab3d has been dead for over 10 years, it may be best to export the models into a more versatile format such as OBJ and then convert to one of the formats I mentioned above. I believe Prefab3D can export OBJ.
- I have not used Flex myself but I found this article about migrating from Flex to HaxeUI which may interest you: Porting our BI Analytics Platform from Flex to Haxe/HTML5 - Haxe - The Cross-platform Toolkit. HaxeUI is actively developed, so it may work well in your situation.
I hope that helps!