I had this problem earlier in the summer.

What we did first was create a giant diff between the trunk and my branch.

What I did then was go through with a copy of trunk and a copy of my branch
file by file.  If I knew for sure I had not modified a file I copied the
exact file from trunk over the outdated one hanging around in my branch.

If it was a file that I had modified then I carefully looked at it to make
sure that the only changes were my changes.  In that case I could simply
keep my file, otherwise I had to update my file so that the parts I did not
change myself matched the trunk.

Finally, I did another diff between the newly committed branch and the same
version of the trunk I started with (this will take long enough its bound to
be updated while you are fixing this, so make a note).
This new diff should only contain your changes and if so, you are done.

In other words, I fixed it manually.  It was time consuming but now I'm much
more careful about making sure my merges are correct :)
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