I had just done the UnrEVOked a few days prior to the update coming out, so here's what I did.
1. Ran UnrEVOked and forever.
2. Titanium backup of all my apps.
3. Nandroid backup of my existing ROM
4. Grabbed the deodexed ROM from this thread -
[ROM] OTA_Supersonic_3.29.651.5 [ROOTED] [DEODEXED] [SIGNED] - xda-developers
5. Nandroid recovery overwriting my existing ROM (no wipe) - same kernal and base means I lost no info and everything was intact.
6. Have my fully updated rooted-rom.
There was some widget clean-up and odd doubling of my icons, but that was easy to fix and cosmetic.
I also had to install the Engineering version of the bootloader in there, too - but that was so I could do the special black-with-white-letters HTC splash screen.
Once you're rooted it's a bad idea to take an OTA update. While Google/Android doesn't care very much if the community hacks, the manufacturers and carriers do care, and if they push updates that break root or your device, they won't care.