Hey, I'm in a similar position (applying for same POI that I already worked with, have taken some classes with the PhD students in that program, had a lot of the same professors).
I have been talking to a few people and a couple of ideas came up:
Assuming they know your work pretty well, ask about areas you can seek to improve
Field dependent: Explaining why you would like to complete a PhD despite having a masters (so the evolution in your goals if it isn't obvious between what careers MS and PhD have access to)
More details about the direction your POI sees your lab going in and ways they are hoping new PhD students can contribute.
Let me know if you have any more ideas, it's definitely a weird scenario.