When is deleted a node than contains product variations type the taxonomy_index table is not updated.
There's no way I can help you with the current description, I don't understand what the issue is, sorry.
I don't think there's a way for Backoffice to interfiere with that process.
Are you using a term reference field, or an entity reference field for your taxonomy?
it seems this is an Inline Entity Form issue.
and it happens for product reference fields with "delete_references" setting set to TRUE.
i don't know why as taxonomy_node_delete() & taxonomy_delete_node_index() do take place.
is there something the IEF controller that doesn't allow the db_delete from taxonomy_delete_node_index() to be executed?
i didn't test for other reference types.
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