Unexpected results from rsync
rsync option -E is OK for the standard but too old version 2.6.9 of rsync which is provided with MacOS X (Mavericks, Yosemite &amp; El Capitan).
But this option -E has another function with standard rsync.

For a user installer version 3.1.2 which is the right one on MacOS X,
then the standard options to maintain ACL and extended attributes are respectively -A and -X.

Here you should use:

rsync -aAvX --progress --delete /source /destination