At some point all files in my working copy got marked with \"S\" symbol as shown below:
$ svn st
M S AclController.php
S InstallationController.php
In my case two sub-directories in the branch were deleted in the trunk. I switched from trunk the branch from the top level directory, and then moved back to trunk and experience the problem with those sub-directories are now in status S
.
I used the answer by @ahnbizcad as a guideline. From the parent directory (which is itself under the top level directory) of the sub-directories:
svn sw
svn sw