In Studio, when defining a document type definition, there is a flag labelled "Deployment Mode". The default value is Merge and the help tip and docs say that this should merge any changes with existing definitions.
We have found that facet contributions are not merged. An example is the nuxeo-media-publishing add on, which adds the facet PublisheableMedia to the Video type. If your Studio project also contains a Video type (as in the DAM demo), the facet is lost at runtime.
In fact it seems any contribution will not be merged because the DocType contribution in the JAR generated by Studio does not have append="true". But perhaps there is a different way of merging.