[Thinkpad Tablet General] jhankinson:
So I successfully updated in ClockworkMod Recovery without losing CWR and without deleting my Superuser.apk and su files by modifying the updater-script in the update.zip. Unfortunately it still messed up my superuser permissions somehow and I ended up having to use ADB while booted into CWR to push and symlink the proper files to get su working again (OTA Rootkeeper wasn't functioning properly because the files were there but the permissions were messed up). I have modified the update.zip so that now it deletes the superuser.apk and su files but keeps clockworkmod recovery. With this and OTA Rootkeeper I think you should be able to update while keeping CWR and restoring root. I will also provide directions here for those seeking to make their own modifications and possibly improve upon my efforts, but proceed with caution.

So what I did was open the zip in winrar and extracted the updater-script. I then edited some lines of code using Notepad++, deleting the ones that referred to deleting recovery or installing a new recovery as well as the lines to delete superuser.apk and /system/bin/su and /system/xbin/su. I also commented out a couple lines at the beginning (assert(getprop("ro.product.device") == "Indigo") because I was getting an error code status 7 when it was trying to perform this check while using clockwork mod. I checked my build.prop and it does say Indigo so I don't know why the check failed but just removing the check was easier for me than figuring out the problem (generally it is not good to remove such checks but I was sure I had the right file). In Notepad++ you must select save as and choose type all files then just save it with the same name. Then replace the updater-script in your zip file with the modified one, I used winrar and chose the compression to just be store (ie no compression). Then you need to delete the CERT.RSA, CERT.SF, and MANIFEST.MF files in the META-INF folder of your update.zip and you sign the update.zip using testsign.jar. Then your new modified update.zip is ready to go.

I think that the reason things did not work out for me is that there are a bunch of lines in the updater script about symlinking and setting permissions for stuff in /system and I think /system/bin/su was originally symlinked to /system/xbin/su which is the real file so things got messed up and I had the files still but the symlink and or permissions were messed up. I eventually fixed this by booting into CWR mounting system and using adb to repush /system/xbin/su and setting permissions and making the new symlinked su file in /system/bin just like the last lines of Dan's Thinkpad root bat file did.

Here is a modified update.zip that should delete your Superuser files but keep your ClockworkMod Recovery. I think that with this file you can use OTA Rootkeeper to make a root backup, temp unroot, then boot into CWR and update to the new OTA then you should be able to reboot and use OTA Rootkeeper to restore root and download Superuser from the market, while keeping CWR through the entire process.

Flash at your own risk! I am not responsible if this totally bricks your tablet! This is the US update, do

not

flash if you are using a tablet from another region! Seriously this stuff could cause problems.

That being said I think it will work. I followed this guide to sign my update.

Original updater-script

Modified updater-script in the update.zip linked above (this one deletes Superuser /system/bin/su and /system/xbin/su but keeps CWR)

Modified updater-script that I flashed on my tablet (this one messed up my su but doesn't delete the files)

If you need a good online file locker join Dropbox here and we'll both get an extra 250mb of space.