[Desire 816 Q&A, Help & Troubleshooting] marth141:
Thanks man. This was incredibly useful. I was about to write everything I did here to get the RUU.exe to work until I realized that FoxyDrew had written basically everything here http://xdaforums.com/desire-816/general/ruu-t2952058

For the sake of redundancy, I'm going to post my steps here.

1. Install CWM recovery and download the nandroid backup.

CWM Recovery.exe for ease

https://docs.google.com/file/d/0Bwq9Di4bqEXkMndWSjNBZjViTjA/edit

This guy has a nandroid uploaded for VM HTC Desire 816.

http://xdaforums.com/desire-816/general/guide-vm-htc-desire-816-root-how-to-t2862470

Now to go through with this. Reboot to bootloader and go to fastboot usb. Run the recovery exe and let it flash on. Then make a clockworkmod backup. Part of this is because we like to have back ups to be safe, part of this is to make the backup folder where you're putting the nandroid backup.

2. Flash the nandroid backup

To clarify, this will not flash like a standard zip file. You'll need to extract it into that Clockworkmod backup folder that we would have made when you made the backup (This will be in your SD-Card). Extract the nandroid zip folder into the clockwork backup folder. DO NOT NAME IT TO ANYTHING ELSE. Here is why... How you'll flash this is by running it as a backup. Inside of your recovery you'll go to backup/restore and restore it. If you name it anything other than what it is named when you extract it, Clockworkmod will not get the right MD5s and will fail restoring every time. This is just how an MD5 work. (If the name is different, then it's clearly a "different file" so the MD5 just doesn't match.)

3. Reboot into the system and remove SuperSU.

This step may be a little annoying. You're going to go back into the operating system and it should be the stock VM rom. However, it'll be out of date. Because of all of our rooting/flashing goodness, we just aren't able to install OTA updates (or at least I never could). So, what you're going to do now is find the SuperSU app, go to settings, and tell it to go through with clean up for a permanent unroot. Let it do it's thing. If it takes longer than a 2 or 3 minutes, reboot your phone and do it again. SuperSU should close and be removed from your phone if the uninstall went right. Now, go back to bootloader.

3. Flash stock recovery, lock, and run RUU.exe

We're getting to the final stretch. In FoxyDrew's post here http://xdaforums.com/desire-816/general/ruu-t2952058 he has the stock recovery listed. Download that and flash it with fastboot. Protip for Command prompt noobs, use win+r and cmd to open a command prompt, find your fastboot folder location and copy it then in command prompt type in cd and paste in the location. This way you'll be able to do everything there. Basically you're writing "cd c:/user/fastbootlocation" so your command line will always stay in that directory.

Anyways, flash on the recovery with "fastboot flash recovery [recovery file].img" let it flash. Once that is done, reboot back to bootloader (you don't have to, but I would just to be safe.)

Once back in bootloader run the command "fastboot oem lock" to relock your device. Now staying in bootloader fastboot-usb, run the RUU.exe that you can download from here http://www.htc.com/us/support/rom-downloads.html (Find the desire 816 from virgin mobile/sprint)

Run the RUU.exe and click through the prompts. Wait for it to finish it's job and viola you'll back onto an updated stock rom without root. Your bootloader will stay say that it is "RELOCKED" however, it will not have tampered or security warning on it.