That does not sound right to me - when you change a workflow for an issue type, all that should change is the workflow.
Could you look at one of the affected issues, click on the "history" tab and look at the exact changes made when the workflow changed - is the workflow change grouped with the reporter change?
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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