Check on the current status and substatus choicelists. You can already see which ones are OOB and which ones are custom. For the custom ones: define what OOB choice it should be and update those via script. When that is done, you can inactivate the old choice options.
Make sure you don't have any flows/workflows/business rules setting the state/substate to any of the old values, because they just will.
Please mark any helpful or correct solutions as such. That helps others find their solutions.
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