I'm successfully on 4.1.2 JB having kept root with ota rootkeeper. Will I keep or lose root if I do a factory data reset in stock recovery?
Factory data reset should never remove root as it does not touch files/folders where su and superuser.apk sit. It only wipes user configurations out (user downloaded apps, user settings/accounts/etc). It does not touch /system/app or /system/bin.
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FDR doesn't replace any system files, doesn't touch any file that a non-rooted user can't access (/system/app and /system/bin non-rooted users can't touch) and just reset user configurations and user downloaded/installed apps.
I'm sure there was nothing wrong with my root install. Every app requiring root worked perfectly, Root Explorer, OTA Rootkeeper, SQLite, TiBu, etc. I wasn't sure what to do after the FDR, but I did update Superuser in Play before testing root. I see that my permissions are wrong on Superuser (in /system/app), but I can't change them without root. Tried the updater and updated binaries, but no joy. Can't restore anything in TiBu without root. Now, I'll have to figure out the Linux root process.
I lost root after a FDR too. I had successfully updated and retained root with OTA Rootkeeper then lost root on the stock ROM. Strange thing is that I still have SafeStrap recovery installed and am still rooted on my LiquidSmooth ROM.
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Factory resets CAN cause loss of root. It is not uncommon for the manufacturer to put a .zip of all the /system partition and wipe/restore that when you do a factory reset.