That would be consistent. I suppose this is a consequence of the constraint that unique buildings can only be built once on a world. You can't, for example, raze your capital and rebuild it somewhere else because a better location opened up. I can't say I hate this mechanic. Actions do have consequences.

My own frustration is that you can't even look at the world before deciding whether to put a governor there or not. It is common for me to have two reasonable choices but one has far better terrain for what I want it to do. In this case I might want to leave this one as a colony because it is so unspectacular and I can't even build a capital.

Every time I've invaded a core world and placed a gov in charge the capital is missing.  I don't buy the "destroyed in the invasion suggestion".  Its not a mentioned mechanic and its always the capital, this seems like a bug to me.    

Hi Paul, any chance you happen to have a save file we can take a look at? We fixed an issue like this a while back, but it shouldn't be happening anymore, so we'd like to hunt down the conditions this is happening.