You use the last incarnation as the basis for your magic-made castle. Of course you are free to add/subtract things as much as you want.
Since Celia, Dario and Dmitri weren't in AOS, do we then assume their Castle is based on the one from 1999?
Although AOS is supposedly the same Castle from 1999 (though it would have changed) which I find ironic because generally the Castle collapses when Dracula is defeated. Julius, however specifically stated he left the VK in the Castle to weaken it. This implies that even though Dracula was completely destroyed, Julius suspected there was a chance that Dracula could return. Or did the Castle simply not collapse because it was sealed inside the eclipse...