If you've got multiple Hyperion Shrinkers in your empire and your ships are (auto-)designed with their provided stacking miniaturization in mind then deleting one will lock you out of these designs. I understand that this supposed to happen because otherwise you could just delete them once you have your final design(s) however it would be nice if there was some sort of notification for this to happen. At best you could just list these ships as sort of impossible to build and in need of re-design. Alternatively you could make buildings which already provide an active effect on your empire as undeletable with a notification showing up with a list of designs which are using it.
That said in GC2 I saw conquering worlds which had a supposedly unique building like this as a trophy effect for your empire but maybe there should be an upper cap of the number of major races which are in the game. Right now I am conquering one Drengin world after another with a Hyperion Shrinker on them, I am also just playtesting the strategical side so just make-do with the auto-designed ships and the game auto-designs everytime it finds a new Hyperion Shrinker :/
PS: I am not listing it as bug because the effect of deletion is no bug per se but it's a major convience drop for the unaware because, y'know you may be forced to re-design from scratch