I can probably give you an answer. Pheonix resurrected Cyke to give her a 'tough love' moment, by showing her that with the Pheonix, she could bring him back and have him with her forever. When Jean, while crying (much to her credit) still refused the Pheonix, explaining to the cosmic big bird, 'she'll never be what the Pheonix wants her to be' ultimately causing the Pheonix to finally relent. As the Pheonix departed, I believe it took away Scott's body to avoid causing Jean any further pain, as it's reason or attempt to manipulate Jean had no longer any value. As Jean and Pheonix are essentially halves of the same coin, I believe Pheonix simply didn't want to see her grieve further and removed the remains, as a balm if you will for it's prior actions.
*But that's just me n my headcannon /shrug.