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Co-author of the article here.

We do support updates for some sources. Deletes not yet. For some sources we do polling which is then dumped on the queues. For other we have listeners that subscribe to changes.

What are the challenges you are facing in supporting this?

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Similar to you, for polling you only see new data not the deletion events so I can't delete embeddings unless I keep track of state and do a diff. To properly support that you/I would need effectively CDC, which gets more complex for arbitrary / self-serve databases.

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