По умолчанию он не удаляет файлы, для этого есть опция --delete
--delete
This tells rsync to delete extraneous files from the receiving side (ones that aren’t on the sending side), but only for the directories that are being synchronized. You must have asked rsync to send the whole direc‐
tory (e.g. "dir" or "dir/") without using a wildcard for the directory’s contents (e.g. "dir/*") since the wildcard is expanded by the shell and rsync thus gets a request to transfer individual files, not the files’
parent directory. Files that are excluded from the transfer are also excluded from being deleted unless you use the --delete-excluded option or mark the rules as only matching on the sending side (see the
include/exclude modifiers in the FILTER RULES section).
Prior to rsync 2.6.7, this option would have no effect unless --recursive was enabled. Beginning with 2.6.7, deletions will also occur when --dirs (-d) is enabled, but only for directories whose contents are being
copied.
This option can be dangerous if used incorrectly! It is a very good idea to first try a run using the --dry-run option (-n) to see what files are going to be deleted.
If the sending side detects any I/O errors, then the deletion of any files at the destination will be automatically disabled. This is to prevent temporary filesystem failures (such as NFS errors) on the sending side
from causing a massive deletion of files on the destination. You can override this with the --ignore-errors option.
The --delete option may be combined with one of the --delete-WHEN options without conflict, as well as --delete-excluded. However, if none of the --delete-WHEN options are specified, rsync will choose the --delete-dur‐
ing algorithm when talking to rsync 3.0.0 or newer, and the --delete-before algorithm when talking to an older rsync. See also --delete-delay and --delete-after.