Issue linking should persist and be visible when a custom hierarchy is in use.

As an example:

Epic Link is used to create the relationship between the Story and Epic. We use "Issue Link" "parent" to establish the link/hierarchy between the Feature and Epic. On import in the Portfolio Live Plan, and after adding the Feature issue type to the hierarchy in Portfolio, the Epic/Story link is honored while the Feature/Epic link is not.

At this point we manually linked all the Features/Epics in Portfolio, and committed the changes. There is no visible relationship added on the single JIRA issues outside of Portfolio.

Ideally the linking is imported along with the issues, and is also updated/maintained when changed within Portfolio.