Did you receive any texts/emails from "Apple" telling you something about your apple account and to go to a link and enter your username and pw?
So they didn't remove it from your icloud account then.
You need to change your iCloud password immediately and you need to turn on two factor authentication.
Did you have a 4 digit passcode, 6 digit, or a character passcode?Apple Justification :
Thief opened you iPhone with correct passcode, which removed it from Find iPhone list. I tested this scenario using iPhone 4, which was not removed from Find iPhone list.
I refused to accept their justification.
Being in Device list is partially useless, as I cannot put it back to Find iPhone list and enable its Lost Mode.
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two factor authentication enabled already. how it can help in my concern now?
Did you have a 4 digit passcode, 6 digit, or a character passcode?
With a 6 digit passcode, the odds are certainly in the owner's corner. However, a thief can get lucky with guesses.iPhone 6 S Plus : 6 digit passcode
With a 6 digit passcode, the odds are certainly in the owner's corner. However, a thief can get lucky with guesses.
If Apple states that the phone was unlocked properly with the passcode, I am inclined to believe them. They have no reason to lie.
Apple Justification :
Thief opened you iPhone with correct passcode, which removed it from Find iPhone list. I tested this scenario using iPhone 4, which was not removed from Find iPhone list.
I refused to accept their justification.
Being in Device list is partially useless, as I cannot put it back to Find iPhone list and enable its Lost Mode.
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two factor authentication enabled already. how it can help in my concern now?
That's weird.
So they removed the find my iPhone icloud lock from it? Putting in the correct pin does no remove it from find my iPhone. They need your icloud password.
You cant view it in the device list any more when you log in icloud?
So they guessed your 6 digit pin within so many wrong attempts before the device locks and resets?
And then after they got in they disabled find my iPhone?
What are the odds of that happening?
Another new member that just registered and story that doesn't make sense...

There's no way this happened as presented. It's like astronomical odds.
I agree with Noob and AJ. While it is possible that someone could correctly guess a 6 digit code, they would need to know your iCloud email and password to do the other things you are talking about. There is no way that they did all that without having access to such information. The odds of someone knowing your iCloud Email and correctly guessing your password, not to mention the 6 digit pin code to unlock the phone is so far into deep space, it is all beyond plausible. The only way that someone could quickly and accurately guess / input such details, is if said person were a close family member and knew the information.
Apple will not provide logs without a court order.I was having same believe until 4/4/2017 10:00am KSA time, the moment I saw device in Find Phone list and in Lost Mode.
see attached apple calls.View attachment 695354
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I am with my family living in Saudi Arabia and iPhone lost during my 10 days visit in Pakistan. iPhone was lost in market during rush hours and found off within 10 min (as I came to know it is lost), and was put in Lost mode with in 30 minutes and was offline until 4/4/2017. Hence, even there is 0 % chance if some one was able to guess correct passcode.
In case my iCloud account was accessed, Apple should be able to provide logs as I requested already.
Easy
If they know your pin to go into your phone
Add a finger print
Then settings/safari/passwords use Touch ID then they can see your iCloud login details
Could you have your icloud login details maybe in your note app or perhaps in the image gallery?
Apple will not provide logs without a court order.
I don't know if the language barrier is making this more incredible than has already been presented but, the odds of someone (not a family member or very close friend who has seen you input such information many times before) correctly guessing your email, password and 6 digit pin code in a matter of moments as you stated is impossible, provided your password isn't "password 123" etc.
What you have stated in the thread isn't adding up correctly.
I don't have any passwords stored or showing there.
And I use iCloud and find my iPhone.
The op story has many holes but I wish him best of luck.
Easy
If they know your pin to go into your phone
Add a finger print
Then settings/safari/passwords use Touch ID then they can see your iCloud login details
So now you're saying its not removed from your icloud account?
Its still there listed in find my iphone?
FWIW, on my phone I have a restrictions enabled, with a restriction on accounts. This effectively disables the ability to go into icloud on an unlocked phone without first going into restrictions, and enabling accounts. It's another level of protection, should I lose my iphone unlocked. The phone is set to lock in two minutes.I don't have any passwords stored or showing there.
And I use iCloud and find my iPhone.
The op story has many holes but I wish him best of luck.