Salesforce released Shield Platform Encryption in v46 on the Email Message Relation object, but the Salesforce metadata API does not yet include support for the
EmailMessageRelation object. This is an issue for users trying to migrate the encryption setting of this object.
Upon investigation, Workbench returns the error
Can't retrieve non-customizable CustomObject named: EmailMessageRelation when you try to retrieve it.
Therefore, any tool using the Salesforce metadata API to retrieve and deploy metadata will have difficultly in migrating the encryption setting for the Email Message Relation object.
If the behavior in the Salesforce metadata API changes in the future, we would look into support for this.