I've been working with UE4 for quite some time and one issue that really gets on my nerves is Modo's erratic FBX behaviour. I run 10.1 and no matter what version I choose (2015 or 2013) when I save my mesh it rerranges IDs order and all my materials inside UE get screwed. Is there a fix for this?
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I figured out a way to (sometimes) reorder material IDs though. Just make a new blank mesh, cut and paste all your geo into it then cut and paste back to the real mesh one material at a time in the order you want. It works most of the time.
The material order seems to stay pretty consistent for me, but it does sometimes reorder itself out of nowhere. And when you get meshes in the same set with a different order... ughh, I share your frustration dude.