I got this working but it was incredibly convoluted. I made four new fields in my entity:
parent_id (calculated value referencing id)
When I export, id and parent_id go into the XML (via the domain to xml mapping)
When I import, that data goes in the temporary fields. Then I use a microflow to loop over the objects and use the temp data to reconfigure the relationships.
If anyone has a better idea let me know.