Windows shutdown to install update while using Windows Easy Transfer

I just got a new computer, and was on the process of transferring my files from my old computer using Windows Easy Transfer.

It was taking a while so I left it on overnight. When I checked on it again, it had reboot to install windows updates. Now, I've got a folder in my Users section that apparently weights 0 bytes, but that is taking up easily 100 GB, which I also cannot access; for trying to do so leaves me with the same explorer window, and unable to return using the address bar or the back arrow.

Is there anything I can do about it?

And do you recommend me try again, or just copy my files manually using an external hard drive?

If it's just files then the external drive is the way to go. If you want to transfer more, like favorites, E-mail, history, application data, then WET is the way to go.

As for the file in your users directory, can you access it after a reboot?
What is the full path name of the folder/file?

I went for the reboot, but the ghost file is still there, inaccessible as before, still making the window unusable if I try to explore it.
The address is C:\Users\enistoja
And it's not just the files but all the software I already have on my old pc (Admittedly I can just reinstall it but I thought it was possible to skip that)

Well I'd first retry using windows easy transfer.

If that fails because of the folder issue (I'm hoping it can fix the folder issue itself) then you may have to reinstall, but this time, do all the updates first.

I've had windows do that to me on my server while doing a 24 hour long first machine backup of gigs of data. Auto update just halts it, reboots the server and it sits there stupidly the next day with a half broken backup

I'm not sure about the cleanup part, but I would have suggested avoided Easy Transfer from the beginning. Why let a wizard decide what's important to you, when it is just as easy to move the data from your drive to an external in the first place?

It can be a real PITA to find all the files for your mail, contacts, IE settings, bookmarks etc for most people. WET really does work and the best part it it copies your actual user account from the old machine to the new one so all those files you did have on a second drive aren't now all permission problems because they belong to a different user...

You can easily get around any permission issue by either using the same username and password, or storing your data in a more organized manner...meaning on a data drive. I can't imagine anyone feeling comfortable letting a wizard decide what's important. What if it misses something? Would those people even notice until it was too late? I wouldn't want my old profile being copied over, because all of my old junk and residual files would be there as well.

The bigger problem is that people don't plan ahead. It's 2012, so very few people should be using POP3 e-mail accounts anymore. That eliminates some of the data right there. Secondly, if a person is storing photos and files on their computer, they should know where...that's a very basic point of computing ability.

I see people being in one of two categories. They would either possess the knowledge to manually back up their data, or they would be asking someone else for help migrating to their new computer.

C:\Users\enistoja is your account folder. Everything under there belongs to you unless you changed your account name on the new computer. If you account name is not enistoja then try taking ownership of that folder and see if you can delete it.

The above link shows you how to add a Take Ownership entry your right click (Context) menu which is the easiest way to do this.