Yes, Ketryx can convert existing Jira native links to Ketryx custom relational fields!

This can be done utilizing an internal conversion tool that will allow the user to group Jira native links based on their two issue types and link type and convert those links to relational fields.  

If you wish to keep your Jira native links, Ketryx can recognize these links if they match the Ketryx relation names, which can also be configured here.