Can you make it so a specific type of link on an issue such as "duplicates" can't be deleted by a normal user, but the user can still add and delete "relates to" links?
Try to implement the JIRA Workflow Properties.
jira.permission.link=denied jira.permission.link.group.1=groupname
Reference: https://confluence.atlassian.com/jira/workflow-properties-189949.html
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