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That might seem a dull question and forgive me in advance but I noticed that when my pc booted in the temp admin from wsus it has many files and programms that I had installed missing! PLus the desktop an the whole appearance has changed to default.
Is that something that will go back to normal as soon as the procedure is done?

WOUTempAdmin is a completely different Windows account. Since your personal account holds your personal preferences and program Shortcuts, that other account looking like default is normal. Yes, it will revert to your account when it's done (WOUTempAdmin will be deleted).

Thanks for your quick reply! I really appreciate it since I got a bit paniced!
For now I am trying like many others to get through the stuck with listing ids of missing updates (last effort was to manually download some of the suggested updates that you guys mentioned in another post)
Damn MS sometimes it's really a hussle!

Yes, they screwed it.

For Windows 7, the official KB3172605 (or the unofficial KB3161647) should be enough to get WU back on track.
Windows 8.1 needs the KB3172614 (or the unofficial KB3163023) to be fast, again.

WSUS purposely creates a WOUtemp account, which is like creating a new user.
So the account it creates, is the same as logging on to the Guest account, where the wall paper and all installed programs are there, but have no user settings. And the desktop and toolbars and quick launch etc, are all returned to factory new. Observe by checking what account you are on in Computer Properties or Network, showing not your normal account logged on.

This option happens when you check automatic restart in the Update Generator interface. Normally it is NOT checked.

However once ALL of the updates are installed it restarts and brings back your default user. The WOUtemp account can then be safely removed if there is left any traces of it.
It causes no immediate harm, they chose this method to be able to turn off any background programs that might interrupt the update process.