Flashing same rom over the already installed one? I have a Note 3 (N9005) with 3.co.uk ROM Kitkat-updated automatically by note 3. it has the following software spec:

PDA/ AP (firmware build version) :N9005XXUGNH1
MODEM/CP(baseband or modem version) : N9005XXUGNH1 
CSC(Consumer Software Customization): N9005H3GGNI1


The phone does not allow rooting by any method, CF or Towelroot so I tried to go back to Jellybean through stock Jellybean using ODIN 3.09. Odin showed RESET but post rebooting original ROM was shown as above with no change. But when I tried Towelroot it worked and root checker showed it as rooted.

Following things were observed:


KNOX is still shown as 0x0 in flashing mode, but Knox does not start at all.
Samsung Kies3 has stopped recognising the phone.
A security notice pops up in notifications area saying unauthorized actions detected.
No other malfunction in the phone. 
Even after removing Towelroot through SuperSU the security warning keeps popping up.


My question is :


Can I flash the same ROM with the above AP/CP/CSC, downloaded from Sammobile to get the phone back to original condition to remove the security alert and restore Knox?
Alternatively Can I flash Vodaphone UK Kitkat ROM for N9005 on this 3.co.uk Kitkat ROM?
Will the new update to Lollipop by the phone thorugh aotomatic updates remove the problem?
Can I flash vodaphone Lollipop UK ROM for n9005 on this phone having 3.co.uk ROM?


Any help is greatly appreciated and would add to my knowledge too, thanks everyone.
It's not a guarantee that the phone will be back to normal (probably you have tripped Knox) but yes it should not be any problems flashing an original ROM over the one you have.
If the system says "Official" when reflashed it should be able to receive updates from Samsung when they are available.

Just remember to empty the cache and in worst case (if the flash does not work as intended) try and reflash with "Re-partition" (though you will probably need the partition file for that then).

Good luck
/Jonas