It's also possible to specify other conflict resolution options, such as `git merge --strategy=recursive --strategy-option=theirs` [0], which avoids the need for manual conflict resolution (and it's "worked for me"). Discarded hunks are still available in the repo history, in case you needed to restore a file/hunk that was discarded in this manner.
[0]: http://git-scm.com/docs/git-merge (be sure to look for the "ours" option for the "recursive" strategy, not the "ours" strategy)