I'm not familiar this specific problem. Health Insight issues involving custom SDA extensions can be tricky, and your set up might need to be reviewed by a support advisor as part of a WRC issue if no one here knows the answer.
Also, since various known bugs have been fixed in recent HI versions, could you provide the full version strings of both the Health Insight and Information Exchange system you are working with?
After an MPI link, an update should be sent to HI for the non-surviving AnalyticsID that has no patient data, indicating it should all be removed. You could see if these are actually being sent, and if so, why the system isn't deleting at that point.
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