Using configuration organizations
In a sharded environment, if an organization wants to inherit Configuration data from another organization, the best practise is to create a third, configuration organization, which eases future data migration.
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For example, if Organization E1 in Colony 1 wants to inherit Configuration data from Organization E2 in Colony 2, introduce a configuration organization E3 in the Default colony. Have E1 and E2 inherit from E3. If you then want to upgrade or migrate data in E1, you simply have to move E1/Colony 1 and E3/Default Colony, with no impact on E2/Colony 2.