This is how I got the update and kept root...
If you have Unrevoked 3 installed:
- Download stock Evo Recovery image (Can't find it anywhere... EVO Stock Recovery? - xda-developers)
- Place the file in root of SD card and reboot into HBOOT (volume down/power button)
- Do the update that HBOOT asks (vol. up for YES)
- Reboot
- Once rebooted, download OTA and install (should work now)
- Once install finishes successfully you can reinstall a custom recovery using the same method (a list of them are here: public:forever [RootWiki])
- Once you have a custom recovery back, you will need to reinstall Superuser as an update.zip through recovery ([APP] Superuser 2.3.6.1 - Now on the Market [2010-09-05] - xda-developers)
- Reboot and enjoy!