This may be the same issue as #IMY-637-46001
https://esupport.stardock.com/index.php?/Tickets/Ticket/View/778097
Whan an improvement with
<IsColonyUnique>true</IsColonyUnique>
is destroyed, it seems to clear that flag for all planets. What may be happening is that you destroy or lose a Prepardness Center somewhere, which resets it for all your planets. It could be (though I haven't tested it) that an AI destroying or losing one also clears that flag for everyone - I don't know if it's player unique or not.
The reason we don't see it for most improvements, is that they often have themselves in <Preclusions>, so if there is already one built, new ones are precluded from being started.
I can certainly confirm that the Prepardness Center also experiences this issue, but there might be another issue with the same effect.
If you experience this issue, check and see if you can build it on every planet.