Circling back here. There are two solutions to this in the short term:
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For incumbent apps / ontologies which can’t be changed, migrate over to using AI FDE instead of Pilot. AI FDE itself can probably help with the necessary steps.
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For new ontologies where you have control over the structure, using object-backed links for all many-to-many joins allows you to continue to use Pilot, as link editing becomes object creation/deletion when using that paradigm (which Pilot can handle fine)