What it looks like in-game 
What sort of models are these and could you please provide or link to model code/JSON?
and it's a baked model
Ah, this uses the Fabric API. Nice.
Could be an issue with normals or light maps, could be Indigo-related or could just be unresolved Vanilla strangeness. I will take a look at this after the next snapshot - I expect it may break everything again at that time.
Does this still happen in 19w44a?
Yes
Has this been resolved?
I have many multi-layer models and they are all fine in the latest builds except for the bugs fixed the latest PR. Would close.
Got it