I destroy the capitol building which then makes other buildings "magically" show up in the available builds.  I want to build those so I queue them up and then I can't rebuild the capitol building.

Thank you for your observation as it gives me another way to approach my problem.

Would it be possible to see some before and after screenshots of the described issue here to better understand?

Here is a link to a zip with multiple save files.  My starting planet is Keleb.

https://we.tl/t-kmCCknS7QM

I will start a new game and do screenshots before and after.

There are some buildings that are not supposed to be built on planets with a civ capital. A supply depot is one.

Edit:

At start of a new game, I can build a capital mainframe and industrial center. If I destroy the capital city, I can build build the capital city, colonial generator, and supply depot. If I build the capital city, I lose the ability to build colonial generator, and supply depot. If I build either the colonial generator or supply depot, I lose the ability to build the capital city.

Personally, I rather have the capital city. It has many bonuses, some of which are rare. The game should mention that these buildings can't be built on a planet with a capital city.

Edit 2:

I should also note that other core worlds don't have a capital city, they have core world capitals. They're not as good as capital cities. Though you can get more capital cities by taking the home world of other civs. By the way, if you destroy a capital city when you have 2 or more, you only get core world capitals back.

So what we're asking the devs to do is reenable an exploit?

I understand what you are getting at now.  I'm going to guess it's probably not easily fixable because it is deeply embedded in the algorithms that determine what kind of a planet it is.  An easy workaround would be to make it a permanent fixture (which I would hate because I usually move it first thing).

It seems that, while having a civ capitol city is the overarching requirement for a Civ Capitol Planet, once it is removed, there are some conflicting rules where you get to go down a branch of the logic tree that was never meant to be traveled.  This suggests that the Capitol Planet is unique and not just an "ordinary planet with a special building".