I am not sure, how the local files can get over-written when you synchronise.(assuming you don't mean "synchronise" in the literal sense. You mean the option that subclipse plugin provides.)
I follow the following protocol for committing a file change.
Do an update of the file. This makes
sure , your local copy is upto date.
SVN will report a merge conflict, if
it is not able to merge the remote
copy to your local one. In which case
you may do a compare with graphical
diff output, and get the remote
changes into your local file
manually. Then do an update. This
time, SVN merge of the remote file to
your local file will succeed.
Commit your file to the SVN repos.