Not sure what you mean by "reference", but all that happens to the issues is that they get stamped with a version which is then released. A Kanban board (usually) excludes issues in released versions from view, but it is just a view of data - the issues are all there to be searched and used as normal in JIRA (and you can get them on boards too, if you drop the "exclude released versions) rule)
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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