Off hand, I'd assume you can use a Script Runner Select List Conversion to create an issuepicker. https://scriptrunner.adaptavist.com/5.0.3/jira/behaviours-conversions.html
Then, you should include this on a screen attached to the Done transition. Finally, you can execute a postfunction that occurs after the issue is indexed. This postfunction should use IssueLinkService to add/delete links as neccesary for your business logic.
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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