We has some files that were being tracked in SVN that we needed to be untracked and ignored, specifically a web.config file, which was being dynamically generated. We removed and ignored the file in a feature branch. We then merged the feature branch into trunk. Then ran svn update on our servers, which caused a tree conflict.
After some googling, the resolution was the following command on the server:
svn resolve --accept working -R .
Thanks to http://www.learnaholic.me/2009/10/04/subversion-resolve-for-tree-conflict/ for the answer.