Yes, we have this a lot with java files unfortunately. To solve it you have to install svn. Then goto the conflicted files. You will see them with the red exclamation mark. Right click and use the SVN repo browser. There you can resolve the conflict. Then you can commit again from the modeller.
The solution was a pretty brutal one; I exported all the changes in the conflicted model to document packages, and then checked out a clean model from mainline and imported the changed artefacts into the clean checkout. I then committed the second checkout with imported documents. Its a harsh but pragmatic workaround ;)