Um script de shell simples vai conseguir o que você quer ...
#!/bin/sh
SRCDIR=dira
DSTDIR=dirb
SRCFILES='find ${SRCDIR} -type f -exec basename '{}' \;'
mkdir -p ${DSTDIR}/NewDir
for FILE in ${SRCFILES}
do
FOUND='find ${DSTDIR} -name ${FILE} -type f'
if [ -z ${FOUND} ]
then
echo -n "Copying ${FILE}..."
cp ${SRCDIR}/${FILE} ${DSTDIR}/NewDir
echo "done"
fi
done