Hello.
So, if I understand the problem correctly, you have replaced the door seal "Edge Protection" and now when closing the window it reaches
almost fully closed then opens again as if it has encountered an obstruction.
Assuming the door seal has been replaced correctly and is well seated maybe try this.
I had exactly the same issue when I first bought our cabrio.
I did not need to replace the seal, although it also had a small tear at the bottom.
So original seal in my case.
If the door was open it would be close OK. As it would not contact the top seal when closing.
I also lubed the glass edge rubber to reduce friction but same problem.
What solved my issue was a gentle push on the window frame away from the car with the door open.
I guess something moved slightly.
It was enough to allow the glass to close onto the top seal without excessive friction.
In my case it was the drivers door window.
Sorry for my long reply.
Hope it may work for you too.
Mine has been fine since, 3 years
Cheers