Default [Q] Binary Counter Question

Since Samsung Introduced 4.3 They said that they have put KnoX on it
So while reading the CF root thread i read that many users got bootloop
so I wanted to ask if flashing the Official software back to the mobile (In case of error)
Resets the Binary Counter or Status to official ? and How does the download mode look like
does it have the Knox Indecator like other Samsung Devices (I used to own an Galaxy Ace plus and now an Xperia ZR user)
I am just asking because I might do that to a friend and we don't want to loose the warranty