Obviously your root permissions time out after a while. This is one of many disadvantages we are faced when running a graphical application such as nautilus as root.
A much better approach for copy tasks with root permissions would be to do that in a terminal, where you stay root by running the copy application with sudo
.
rsync is just one of many file copy services but one with tremendously many options, the possibility to copy over network, have it resume on errors, skip already existing files on the destination, or let it exclude files or directories.
The basic command for rsync is very simple
sudo rsync -a source/ destination
where source and destination are the corresponding mount points (or network locations), and -a
is for a sensible "archive" option that includes all options rlptgoD
.
Only one thing that always confuses me a bit is the slash /
after the source directory which tells rsync to not create this directory on the destination but copy all of its content instead.
There also is a graphical interface grsync for those who dislike the terminal too much. I use grsync because it allows to drop-down select from different copy profiles I had set up for backup purposes.