Dude, did you even see the movie? Its downright stated.
Diva has the Quantum Cube the source of Prana
1. Kaiba didnt have obelisk on his deck, since all god cards dissapeared with the pharaoh. He summoned Obelisk right out of his head.
2. Before starting their duel, Diva tried to bfr/kill Kaiba with the Quantic Cube, before being blocked by his new duel disk.
3. Good enough, not time travel, maybe dimension hoping?
4. When he returned for a brief moment to summon Mahad and defeat corrupted Diva, he reversed the damaged done.
inb4 "But the pahraoh has the power to take away the QC´s power!" He has, but if his power was just mean to "take away their powers" the universe wouldnt have been restored, only the desctruction would have been stopped.
Aka- Atem restored/reversed universal levels of power.
5. Yeah, but it still destroyed a dimension, and you should know that you cannot prove it was just room level either since we do not see the outside.
6. From deleting Joey based on his memories, which are conceptual and metafisical.
If you delete someone by deleting his memories directly, its not brain damage or mind manipulaiton, its conceptual manipulation.
7. Atem saving Joey from being destroyed by Diva, he entered his memories and reversed all damage on Joey´s memories.
Remember, they were being FORGOTTEN by Joey, and once he forgot a single detail, the memories were GONE, but after recovering from Diva´s attack, he has his memories back. That means Yami can revert the damage done by prana on a conceptual level.