I am very sorry for your loss and for your granddaughter. She apparently can see auras. Blue is a very spiritual color; it means he felt peace and calm at the time of his passing. Green is a healing color, so maybe he felt whole right before he passed. Or he was a healer or doctor of some sort in life? By the time she saw the black, his soul had left his body, so he was already gone.
I can't see auras myself, although I have been with people I love at their time of death. So I don't know if the aura goes back to all the colors after the soul goes on its journey to wherever you believe. So I can't answer why it didn't go back to rainbow.
But the black is not bad, it's just the absence of color, and that is normal, since by that time he already left his physical body. The blue and green are both spiritual and calming colors, so at least he was feeling comfortable at the time and was not suffering. Blessings to you during this difficult time.