Ari Jaaksi, the head of webOS & services and HP announced on his blog here that they are releasing a new software update (3.0.4 - 77) for the HO TouchPad. It is an OTA update and has lots of perforamce improvements, better support for camera, UI updates & tweaks, and more apps!
So go ahead and update your TPs, but if you have HomeBrew and custom kernel & patches, then worry not. According to this forum post and this one, and this wiki page, updating your home-brewed TP is harmless and you do not need to do anything special. The patches may just stop working for some time till the latest updates of those patches are available and get updated. Also, some of the issues being addressed by the patches may also be taken care of by the new update.
So, as Ari says - enjoy the new update - no strings attached ;)