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Push in on the top of the window a little and close the door easy. The window will go back in the channel.
Sounds easy. If you've actually done this then great, this could help other forum members if they find themselves in this rare situation (it's not covered in the owners manual). I have to admit I was working in the dark of night, hard to see what the heck I was doing and I apologize to the world. Wouldn't be the first time I made a fool of myself. But, if this is theory, then I would need to challenge it. From my experience, there was no way that window was going back into the channel. Either way, we exposed a peculiar aspect of these emergency systems that most are not aware of. Not a bad thing.
I'm annoyed by the "stealth" nature of the Emergency handle and its location.
If this was an airplane, there would be a foot-long red and white arrow on the door, pointing at the handle and saying "Lift Handle for Emergency Exit".
That's overdoing it, but it took me a year to figure out what the little drawing on the handle was supposed to show, even though I knew how it all worked.
I did this last year when the car wasn't driven for a while and the battery went dead. Opened the hatch and pulled the door release. Closed the door and didn't realize there was a channel the window fit in.The sight of the window on the outside of the channel was not pretty. Pulled release again pushed in at the top of the window and while closing the door easy and got it to fit in the channel. Took a little work, but it can be done. You can also open the door by pushing in the window at the top.