Uh oh, I need to look for a box with a checkmark in it to keep the components in there??? Okay, I'll play and take a look-see, must be miniscule.
It's in options, under Interface-the check box is Remove functional components when upgrading a design and if memory serves it is checked by default, so you'd need to uncheck it to truly upgrade an existing design, otherwise you're just upgrading the hull.
My apologies for not being more specific in my earlier post; I've got a little too much going on at the moment.
I had the same problem with Hyperion Shipyards, I thought that the Starport was enhanced by the shipyard, INSTEAD the Starport was GONE after building the shipyard,.... that is just &$*@^$&* stupid. A ship yard builds ships, that's all it does, and yet you can knock down a starport and make it UTTERLY USELESS with NO warning. F L A W !
This is a flaw in the description of the Hyperion Shipyard, yes. But now you know that it doesn't replace a starport, and in fact you don't need to (and there's no reason to) "upgrade" a starport into a hyperion shipyard. Further, you can "upgrade" any building of any type into any other building of any type, so the building "upgrade" system doesn't really work that well-the tiers only apply to what auto upgrading is done when you have auto upgrading for that planet enabled.
My understanding of this problem is that the starport object is hardcoded, but it does seem like a bit of an oversight that the hyperion shipyard is not allowed to build ships, in retrospect.