This procedure should work for any CDMA or GSM Evo 3D/V that is S-OFF. There is no way to get an S-ON device that has been HTC unlocked back to 100% stock since relocking the bootloader will result in a status of "relocked".
Here are the steps to do it:
1. Flash the "query_bootloader.zip" file attached to this post in recovery. If the status message shows your bootloader is "unlocked" or "relocked" flash the "lock_bootloader.zip" file from the same post to reset it to "locked".
2. Download an RUU.exe (Windows) or RUU.zip (bootloader) file for your model from this page and flash it using the appropriate method.
If you use the .exe version from Windows it works best if you put the phone into "fastboot USB" mode, and you may have to cancel the RUU utility and restart if it hangs after flashing the stock bootloader when you start with a custom hboot installed.
To flash the RUU.zip via the bootloader it must be renamed to PG86IMG.zip and placed in the root of your SD card, and may need to be flashed twice if a custom hboot is installed the first time it is flashed.
I recommend using the latest version for your model but any compatible RUU can be flashed while S-OFF. It's also a good idea to boot the ROM without doing any setup after flashing the RUU to make sure the ROM has been reset to the stock version.
3. Confirm that the bootloader shows "***LOCKED***" on the top line of the screen and the HBOOT version is a stock bootloader for your device.
4. Issue the "fastboot oem writesecureflag 3" command from a PC.
Note: Make 100% sure you have the stock bootloader installed before issuing this command or you will brick your phone.
Your phone will now be 100% stock.