After many attempts at trying to, unsuccesfully, merge branch changes into my trunk using SVN I came across a working solution, courtesy of http://crunchlife.com/. Here it is:
Step 1: checkout the trunk to a working folder
svn checkout file:///repository/project/trunk /home/project-trunk
Step 2: Perform a merge bewteen the SVN repos trunk and branch with onto the checked out trunk folder
svn merge file:///repository/project/trunk file:///repository/project/branches/my-branch /home/project-trunk
Step 3: Commit the changes on the trunk folder back to the repos
svn commit /home/project-trunk -m"merging my-branch into trunk"
Step 4: Sit back, relax and be happy
