If we create an external merge feature, all layers from the merged model are available in the part. But if we make some changes in the merged model, like move an item to other layer, this is not completely reproduced into the part (item is added to the new layer but it is not removed from the old). We need always additional work to make the layers correctly displayed after a change. Some times is better delete the layers from de part and regenerate the model so the layers from the merged models can be correctly recreated.
Layers should be completely associative from merged model to destination part.