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.
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