The -u switch in rsync does not work between different file systems so it seems. It is supposed to ignore existing files in the destination directory, but it doesn't - well at least it doesn't between UFS and EXT3 in my doings. Using the --size-only switch along side -u is a work around. Example rsync for my reference: rsync -airu --size-only /source/dir /dest/dir -a archive mode -i itemise change summary -r recursive -u ignore existing files man rsync