I had a nightmare recently with SVN refusing to update a file, then skipping a folder. Here's what worked for me.
SVN refused to update a particular file 'template.html' in a folder 'newsletter' deep in a tree. It just ignored it.
Odd. I delete the file, template.html. Ran update again. Nothing, just says up to date revision 999.
I'm under pressure to get this done NOW so start panicking. I delete the folder 'newsletter' and run the update again.
Now I get 'newsletter' skipped messages.
After a long, long set of attempts to get this back this finally worked, go into folder that had 'newsletter' in it:
> svn revert --depth=infinity
> svn up --force foldername
That restored the folder and contents and the problem file. From then on svn updates ran fine.