This SO question might help you. The answer it gives is:
Never, ever, forget to commit a run of
svnmerge.py before doing something
else. Combining a merge with other
edits is a recipe for a disaster, and
the disaster is what you see in the
question.
The SVN Book also says:
Whatever the case, the “skipped”
message means that the user is most
likely comparing the wrong two trees;
they're the classic sign of driver
error. When this happens, it's easy to
recursively revert all the changes
created by the merge (svn revert
--recursive), delete any unversioned files or directories left behind after
the revert, and re-run svn merge with
different arguments.
And then there's this blog post that claims:
I finally found a posting with
instructions on how to merge in spite
of the “Skipped” error message… so I
tried it, and it worked (in spite of
the misleading messages). The trick
really is to ignore the messages.
Note that following the merge, files
that are in the source branch and not
in the destination branch need to be
svn added before they will end up in
the destination.
It seems the general consensus is that you need to do a proper merge of the file in question.