When you log out and relog in studio, none of the schemas that have been contributed appear in the extra schema of a document definition even if it was added to the document definition before.
Blocker because it will lead to errors if the schemas was used in the layouts...
To reproduce, create a new schema. log out, log in. Go to a document definition. The schema is not available in the extra schemas.
You can make a schema reappear by going to the schema definition and resave it (even without modifications), but you still have to reassign it to the document definition.