The ID of a configuration object "X" deployed with CMJ is differs from the id of the same object on source

Problem:

Certain scripts or other custom configuration that is not supported by CMJ rely on configuration objects' ids and these functionalities don't operate correctly after deployment with CMJ

Cause:

CMJ does not have control on configuration object ids, as they are generated by the underlying framework used for persistence. 

Solution:

It's recommended to refer to configuration objects by name whenever possible. 

CMJ also provides a setting called "Persist deployed snapshot to current system native ID mappings", available in the General Settings page.
When it's enabled, the add-on generates a mapping of the ids coming from the snapshot to their counterparts on target instance. This mapping can be used to update the ids post deployment manually or through a script.