You find that Territory Realignment Runs do not Update the Owner field in an realigned Account's related Opportunity.
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The Realignment Run was not developed to update Owners in Objects, but only updates territories where it has to (Account and related items).
The Owner field maintenance is based on regular party determination in each Object.
Assuming Opportunities are initially fine-tuned under 'Maintain Involved Parties', it will already determine the Owner based on the Territory Owner.
Once the Territory Realignment takes place, and the Territory of the Opportunity is updated, the Owner update will remain based on the Fine-Tuning rule as the Uwner is determined based on this new Territory.
However, if a Lead for example, does not have this configuration, then the realignment run will not affect the current Owner maintained.
This is the designed behaviour.
Account Opportunity, Related Opportunity, Opportunity Owner Determination. , KBA , LOD-CRM-TM , Territory Management , Problem