OMG, this is such a bad change apple has done. I am using iOS 9.1 on iPhone 5S. I had around 450 photos in my camera roll, I was trying to transfer those to my PC, on my PC I could see so many .AAE files which I was not able to open so I thought these are just side extension or edit backup etc etc so I deleted those from camera role assuming the number of photos will remain same. All sudden I loosed 150 photos & there were also not in the recycle bin because I deleted from camera role directly. So now I have loosed my best 150 pictures. *****!
I wanted to make sure again that deleting .AAE file deletes original image from iPhone, So I did a test. I clicked 3 photos using my iPhone,
1 - Normal light, 2 - Chrome mode, 3 - Fade effect.
Then I connected my iPhone with PC & looked into camera role, Chrome & Fade were reflecting as .AAE & not visible on PC, when I deleted those 2 photos, those were also gone from iPhone & I was only left with one photo which was taken under normal light effect (the default camera effect).
So if you want to copy photos from iPhone to PC then do not use effects, else it would become .AAE which is of no use except iPhone. If you guys found out any solution then please do let me know