I ran into that problem too. I opened up a terminal and ran the following command:
sudo nautilus /var/lib/apt/lists/
That will open up the folder containing all of the files that need to be changed as root in nautilus. As root you can double-click on a file to edit it, or for some it may be necessary to right-click and select Open With Other Application... and then choose the text editor you want to use to delete the contents of all of the files--I used gedit b/c its simple and it works.
I ran into that problem too. I opened up a terminal and ran the following command:
sudo nautilus /var/lib/apt/lists/
That will open up the folder containing all of the files that need to be changed as root in nautilus. As root you can double-click on a file to edit it, or for some it may be necessary to right-click and select Open With Other Application... and then choose the text editor you want to use to delete the contents of all of the files--I used gedit b/c its simple and it works.