Summary

After configuring a custom issue hierarchy within Advanced Roadmaps, when loading the issue outside of Advanced Roadmaps, the hierarchy is not respected.  For example

• If an issue is linked through the standard interface as the 'Parent Of' another issue, these issues do not show as linked within Advanced Roadmaps. 
• If an issue type is set above the Epic issue type in the hierarchy, when adding issues to an Epic via the 'Issues in Epic' field on the Epic, the issue type above the Epic in the hierarchy can be added to the Epic as a child.  

Environment

All Jira Server/Data Center installations with Advanced Roadmaps

Cause

There are three different types of issue links within Jira:

• Parent Link – This is used by Advanced Roadmaps to connect parent and child issues.  This will respect the custom Advanced Roadmaps hierarchy. 
• Issue Link – This type of link is used when you leverage the 'Parent Of', 'Child Of', 'blocks', 'is blocked by' type of issue links.  These do not link these issues in any type of hierarchy, it simply connects the issues together to make it easier to navigate between linked issues.  The 'Parent Of' or 'Child Of' options here simply add a bit of metadata to help the user identify how the issues are linked together.  
• Epic Link – This type of link is used by the standard Epic issue type.  It is designed to function as if the Epic is the highest issue in the hierarchy regardless of the Advanced Roadmaps hierarchy.  This type of link would be provided by Jira Software regardless of Advanced Roadmaps being installed with Jira.  So any custom issue types that are set as 'standard issue types', will be linkable to the Epic as children via the Epic link.  

Solution

Depending on the specific scenario there may be different solutions the issue.  However in order to leverage an Advanced Roadmaps custom hierarchy the 'Parent Link' field must used.  That is the only issue link that will respect a custom Advanced Roadmaps hierarchy.