I had an interesting issue I thought I'd share with folks in case they run into it. I have an N900W8 on the Rogers network. I used CF Auto-root to root, installed Philz recovery through Odin (3.07). I backed up the stock OS using Philz, then installed CM11 M5. I played for a couple of days, and then decided I wanted to head back to stock. I'm probably going to sell the phone soon so I wanted to make sure everything was clean. I restored the stock ROM, and when Philz warned that the stock ROM would likely overwrite recovery, I let it. I booted into my previous stock ROM and all was good. I checked software update and it said "your system has been modified". Shoot. I boot back out into download mode and see System and Firmware are set to Custom. All stock 0s everywhere else though, Knox hadn't been tripped. I was about to flash a stock firmware through Odin and I thought.. I wonder if I could use Kies? Sure enough, I fired up Kies 3 and did a Firmware Upgrade and Installation and 10 minutes later I had a stock phone. System and Firmware back to Official Samsung! All I did was boot the phone up in my restored stock ROM, plugged it in, ran Kies 3 and said "Firmware Upgrade and Installation" done.
Hope that might be helpful to someone!