It is almost always the case that "when root cannot do something root should be able to do, the problem is selinux".
As it's been months, the situation has probably been remedied, but if someone else has a similar problem and see this post, I recommend running "setenforce 0" which will put selinux in "permissive" mode until the next reboot (or until "setenforce 1" is run). See if that fixes it such that you can cd into Desktop.
If that fixes it, then you will need to either restore the selinux context for /home/user, or change the selinux policy for files under /home.
cd
into them?cd
will not produce any output if successfulls -l
say? Guess: Desktop is a stale link...Desktop
, it's not that. And it is a directory and not a symbolic link.