It can't damage the PIT partition by itself.
I had the same missing PIT problem on my old Galaxy Player 5.0 because i entered a Motorola partition code in the Terminal Emulator (Don't ask why....LMAO)
Yeah i couldn't fix it and i got a replacement.
Maybe check the symptoms of an Insane chip,some Note 2's have a hardware issue, maybe the Insane chip became "Insane" ? lol