You'll need to make sure the process is terminated on the OS level. Then, you can use the following command to unregister the PID from Ensemble:
Do ##class(Ens.Job).UnRegister("<config name>",<PID>)
Restarting the production should also work, but you might need to force shutdown the production.
You'll probably need to copy over, from the base schema, all <SegmentStructure> that reference the custom code table, and all <MessageStructure> that reference those segments, and all <MessageType> that reference those message structures. Please give it a try and let us know how it goes. In case it's still not working as expected, please post the full custom schema and the base schema for further discussion, or contact WRC for further assistance.
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