Copy problematic folder into some backup directory and remove it from your SVN working directory. Remember to delete all .svn hidden directories from the copied folder.
Now update your project, clean-up and commit what has left. Now move your folder back to working directory, add it and commit. Most of the time this workaround works, it seems that basically SVN got confused…
Update: quoting comment by @Mark:
Didn’t need to move the folder around, just deleting the
.svnfolder and then svn-adding it worked.