[X Style (Pure) Q&A, Help & Troubleshooting] robn30:
So I wanted to create a thread dedicated to performing this function. I know as someone who does this quite often, I like to have all my ducks in a row to ensure everything works perfectly. I'm not big on fragging my phone and then frantically trying to find a way to undo all the chaos. I do a lot of research and ask a lot of questions before doing anything.

On that note I would like to first thank all the amazing people on here, whether they be developers or just experienced Tech Guru's, everyone is always a big help. I take absolutely no credit for any of the awesomeness that can be found on XDA, I'm just creating a thread that I hope will help folks find everything in one place for this function. So here we go, I'm going to explain the way I did it, which is the way I have been doing stuff like this for years. I have a preferred method as it has always resulted in perfect flashes and no bricks, not even soft bricks. So I feel it works pretty well.

Just so it is understood, this is for the Moto X Pure, which has been bootloader unlocked and has TWRP and root installed. Also it should be noted that you need to have Developer Options enabled and USB Debugging enabled. You should also be familiar with the ADB process, to some extent, maybe you have at least heard of it;).

Steps to follow:

1. Use Titanium Backup and backup all your User Apps, NOT SYSTEM APP's, system apps will not restore across updates and will most often corrupt your new install.

2. Make a Nandroid backup using TWRP, I backed up system, boot, data, and EFS, but I don't think EFS is necessary.

3. Make sure you have the Motorola Drivers installed, get them from here http://www.motorola.com/getmdmwin

4. Get Shawn5162's Restore to Stock Tool, I know others have said it's not necessary to perform a complete restore, but this is part of my process that I have always done, and it's always worked. Get it here by using one of the mirror's created by patt2k in post 6, and don't forget to thank him for the mirrors http://xdaforums.com/moto-x-style/development/windows-tool-moto-x-style-pure-edition-t3199905

5. Unzip Shawn5162's zip to a folder on your desktop, and before you move onto the next step, make sure you have backed up everything valuable on your phone, such as pictures, messages, etc..., because everything is going to be erased in the next step, except for the stuff on your MicroSD. I'm so anal, I even remove the MicroSD before flashing. Connect your phone to your computer using a USB and make sure you have USB debugging enabled under Developer Options.

6. Inside the folder you created run the FLASH-ALL.bat, which will reboot your device to the bootloader and begin the restore to stock flash. This will remove root and TWRP, but will not remove the fact you have an unlocked bootloader. Your phone will reboot when complete and should boot back into your system within a short period of time.

7. Once you are rebooted, you may need to do a little setup before you get the message that a System Update is available. DO NOT waste your time installing any apps, wait until you have full root on MM before doing any of that. Once the Update message appears, accept it and download the MM update file, then install it once it is finished downloading and asks if you want to install.

8. The update takes about 20 - 25 minutes so be patient. Once complete your phone will once again boot back to system, now you have MM in it's complete unrooted greatness.

9. Now go into settings, about phone, and tap on build number a bunch of times to enable Developer Options. Then go into developer options and enable USB Debugging.

10. Next download a bunch of stuff from the following links, if you desire to install TWRP and regain root.

TWRP 2.8.7.1 here https://dl.twrp.me/clark/twrp-2.8.7.1-clark.img

Modified Boot Image from here, required to perform systemless root :cowboy:, not sure about the Cowboy hat dude, but click on him, it will download the file.

SuperSU 2.52 from here https://download.chainfire.eu/743/SuperSU/BETA-SuperSU-v2.52.zip?retrieve_file=1

11. Next copy the modified boot file and SuperSU file directly to your internal or external SD on your phone, either works fine, although I prefer my External SD.

12. Next copy the TWRP file you downloaded into the same folder you made for Shawn5162's files. This folder has all the adb and fastboot files you need to perform the TWRP flash. Now hold shift and right click and choose open a command window here. Then ensure your device is detected by running the command adb devices, it should show your phones S/N and the word device. If it doesn't, you may need to look at your phone and respond to the prompt about allowing your computer to have access to adb. Try the command again after that. Then run the command adb reboot bootloader, which should reboot your phone to bootloader fastboot mode.

13. Once it fastboot mode run fastboot devices just to make sure your device is still detected, then run the command fastboot flash recovery twrp-2.8.7.1-clark.img. That will flash TWRP to your recovery partition. Then type the command fastboot reboot twrp-2.8.7.1-clark.img or use the volume rocker to toggle to recovery then select the power key to boot to it. Make sure you choose the slider at the bottom to allow modification. Once on the main screen you can choose reboot and then select recovery. This makes sure that you have booted to TWRP at least once, and ensures by rebooting to it, you can get back to it.

14. Now perform a Nandroid Backup, using the TWRP Backup option, of your completely stock MM system, data, boot, and EFS partitions. Enable compression if you like and store it to your External SD if you have one. This allows you to have an unrooted backup on your SD, which is good for future updates. After the Nandroid is complete now flash the modified boot image zip using the TWRP Install feature, and when it's complete, then flash the SuperSU zip file. After I always perform the option to erase Dalvik and Cache, I just think it is a good thing to do, it's probably placebo, but I do it anyhow.

15. Go back to TWRP Home and choose reboot and select system. Your device will reboot and you now have a fully updated and rooted Moto X Pure on MM.

Thanks go out to all the folks who have contributed to the many threads that contain this information. Special thanks to Shawn5162, DaMadOne, Chainfire, and Hashbang173 for their awesomeness. Hope this helps folks that are concerned about performing these procedures. I can say that it worked perfectly for me with no issues at all, but of course I take no responsibility if it doesn't work for you and causes your device to fail. Again these are similar steps I have taken in the past with other devices and I have never had a single brick, so hopefully it works for others as well.

Enjoy!!