First, at the end of original portal we can see a storage area containing numerous cores with various retinal colors. Second, companion cube was incinerated too, but Chell received it intact (almost) at the end of the Portal 2. I see no reasons why couln'td personality cores be saved as well.
but your forgetting that the cores were made for GLaDOS and those cores are not and Aperture has numerous ammounts of cubes. in portal 2 GLaDOS says they have warehouses full, but the reason why they cant is because well, its an incenerator.