I'm just a newbie, so take what I say with a grain of salt.
I don't know what to do about your Ubuntu installation and file partition.
Apparently, most patches use Auto Update Patch Technology (AUPT). These patches do not have to be removed before updating your webOS. But not all of them use AUPT.
I saw a recommendation that when an update is announced, one should wait 24 hours.
During this period watch the @webosinternals twitter feed for further instructions. They should tell you which patches should be uninstalled before updating.
Important note: I have read warnings that you should first remove all your themes before removing any patches.
If you are paranoid, you can make a "saved package list" of all your current patches. This is done via the Emergency Patch Recovery (EPR).
Remove all Patches and Themes - With WebOS Quick Install:
1. Remove any theme: Click Tools → Themer → Revert to Default
2. Remove patches: Click Tools → Tweaks → Run EPR → Luna Restart
Remove all Patches and Themes - With Preware:
1. Remove themes: Tap Installed Packages → Theme → Tap your theme → Remove → OK → OK
2. Remove patches: Tap List of Everything then type "emergency" and tap Emergency Patch Recovery → Install
3. Restart your Touchpad
After you have removed all patches and themes, you then perform the webOS Over The Air (OTA) update, then reinstall your patches and themes.
If I have made a mistake here, please correct me.