I don't fully understand the current situation. Perhaps a photo would explain it better?

If what I think is the case, that your panoramic roof is stuck in the 'tilt' position and won't close, what is likely happening is the anti-trap mechanism is being activated.

First try the re-initialization procedure. Put key in position one, and push the sunroof button (like you would to get it to tilt) and hold it for a while (something like 2 minutes total I believe). The entire thing will cycle through all its possible movements. Once it is done, and only then, let go.

If the reinitialization procedure doesn't work because the sunroof is stuck, then start the car (you want to have the engine running because you don't want to drain your battery during this if ends up taking a while) and keep pressing the button in any direction to try to get the roof to close. It might take 50 tries but hopefully it will work. Just keep at it (ie. push the button in the next direction before the roof even stops moving from the last push). Once your roof is closed, turn off the car and do the reinitialization procedure describe before.

If none of this works you need to go to the dealer and get the thing realigned.