Rsync link-destination remote server

Use the -R or --relative option to preserve the full path.

You could use -i --dry-run to get the list of changes between your two folders and then only keep the files that have been deleted.

However, most people do backups with rsync by first doing rsync and then cp -al of the backed up data (e.g. current) into a different directory (e.g. archive). The -l argument tells cp to not copy the data but to just create a hardlink. That way, you have the same data available under current and archive, but every file occupies the disk space only once (e.g. without the overhead you are experiencing now).

Later, as soon as you again rsync your server to current, rsync will update the all the files that have changed and delete the files that have been deleted. The files in archive, however, will not be touched.

Of course, you can create as many archive folders as you want. Also note that rsync offers the --link-dest option, which can automatically create the archive folder during the rsync run, without having to run cp -al. See the man page for more information.