I searched and really couldnt find a clear answer for this...I'm on 3.2.2 now, I'm not going to upgrade until there is and untethered JB for 4.2.1. That being said, I'm wanting to know the best way to do an absolute total wipe of all files, including all jailbreak and jailbreak app files so I can do a clean install of 4.2.1 when the time comes.
wouldn't restore/update completely wipe off everything on the ipad/iphone?
I read on another website that someone said that updating will still leave some jailbreak files behind, but i couldnt confirm cause it was a a really old thread. I know that when I updated from 3.2.1 to 3.2.2 that alot of the cydia apps were left behind, but cydia didn't recognize them as installed even though they functioned. Ive been experiencing some weirdness with the iPad lately that no one seems to be able to figure out.
You are correct.
An UPDATE will leave the filesystem intact, so even though you cant see or use them, your jailbreak files would still be there... As you discovered, this can cause some unusual things to happen if you subsequently jailbreak the new OS. You could even end up with incompatible jb apps which break your installation at a later time...
A RESTORE will wipe everything and restore your iPad to factory freshness...