Hello Everyone. So I was able to fix my issue today (Thank the Lord).
I spent good 4 hours to figure it out. First I remove the bottom part of my back seat to see how can I see the luggage part when the trunk is closed (Top Down Position). So I saw nothing (Lost 1,5 hours).
Then I remove the head rest area completely. That helped me to figure it out how the locking system working!
So what happens is when your Hard Top roof package is completely stowed, while the rear trunk cover is closing, it locks up the roof package from this front locking latch!
So mine was locking but It wasn't locking the way it is supposed to be. Since I can see how it looks like when the trunk is close, I tried to move the roof package to see it is loose or locked, So mine was locked and was not moving. That means, even I was getting HardTop malfunction, Hardtop is not locked, SO I was still able to drive without an issue at all! That's what I figure on my case! And then I realize how to fix it.
All I can say is you do not need to spend even 10 minute to fix this issue. You do not need to remove any panel to reach up the way I did. And of course YOU ARE NOT DROPPING YOU CAR TO THE DEALER!
If your issue is, Your top is closing normally but when you TOP Down everything seems normal but your windows are not rolling up back after the top is down, Most likely your issue is same with mine!
All you need to do is try to top up again, when the trunk lifts up, stop the process (Do Not let the roof package to lift up), And then you will see the lock points if you look at from the rear seat. Each side has 2 screw.
Unscrew them, then try to top down again. So it will self align itself then try to top up again. Do not let the roof package lift up. Screw them back tightly. That should solve the problem!
Mine works like a charm now.
Here is some pictures!
All cleaned Up. Hope it helps the LEGEND E9x Community!