So let me get this straight: If I'm rush-buying a building over an existing one, it will cost less BC if he original building was build ad not bought?
In essence, yes. When you rush buy a building over a built building, you get the full amount of social production invested into that building (which is always at least equal to and probably slightly more than the cost) applied as a discount, before the rush buy formula is executed.
When you rush buy a building over a rush bought building, you only get what has not been previously credited towards rush buying (which in the case of the first one is all of it, but beyond that is not).
So, rush buying over a built building will either 1) rarely, but possibly, cost exactly the same amount as rush buying over a rush bought or 2) cost less, yes (simply because more money i.e. social production has already been invested into it).
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It takes less production to rush buy an upgrade as opposed to an empty tile, but they will take the same amount of time to build, as you ONLY get the discount for rush buying. If you build, you pay the FULL amount of the new building. Even if you're upgrading from a Discovery Sphere (250) to an NLC (500), if you build it it will still cost you 500 in production.