This has been an issue since release, and it's maddening: empire-wide and planet bonus buildings are being abandoned by migrating POPs, requiring not only micromanagement, but preemptive scanning of all applicable planets because there is absolutely no warning when it happens. Your entire empire could end up losing happiness, habitability, research, food, etc. etc. bonuses without you ever being made aware of it - not to mention that it makes very little sense for those buildings to stay unoccupied if there's any way to get them back up and running without causing the relevant planet to starve.
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