i had a similar issue recently. if you use a custom lineage resource to import those relationships, it should work ok.
if you were using lineage*.csv within the custom resource, i think that is only importing dataflow links at the moment.
you can take the same lineage*.csv file(s) and remove the com.infa.ldm.etl.ETLContext column
Thanks a lot Darren!
I was not aware of the option to do that using the custom lineage resource (it's not the most straight forward option as you already declaring the links in the resource itself).
I found another kb that explains how to do that in case someone will face the same issue in the future.
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I can confirm that even with v10.4.1 - there will be no changes to lineage*.csv processing for non data/control flow relationships.
you will need to create a custom lineage resource to import these relationships, or use the API directly. My preference is to use custom-lineage so you can easily purge/reload etc...
the custom lineage resource type can have any valid relationship in the Association column - and it can use either connection assignment or direct linking via object id.