Я думаю, что вы ищете вариант -m.Со страницы руководства:
-m, --prune-empty-dirs
This option tells the receiving rsync to get rid of empty directories from the file-list, including nested directories that
have no non-directory children. This is useful for avoiding the creation of a bunch of useless directories when the sending
rsync is recursively scanning a hierarchy of files using include/exclude/filter rules.
Note that the use of transfer rules, such as the --min-size option, does not affect what goes into the file list, and thus
does not leave directories empty, even if none of the files in a directory match the transfer rule.
Because the file-list is actually being pruned, this option also affects what directories get deleted when a delete is active.
However, keep in mind that excluded files and directories can prevent existing items from being deleted due to an exclude both
hiding source files and protecting destination files. See the perishable filter-rule option for how to avoid this.
You can prevent the pruning of certain empty directories from the file-list by using a global "protect" filter. For instance,
this option would ensure that the directory "emptydir" was kept in the file-list:
--filter ’protect emptydir/’
Here’s an example that copies all .pdf files in a hierarchy, only creating the necessary destination directories to hold the
.pdf files, and ensures that any superfluous files and directories in the destination are removed (note the hide filter of
non-directories being used instead of an exclude):
rsync -avm --del --include=’*.pdf’ -f ’hide,! */’ src/ dest
If you didn’t want to remove superfluous destination files, the more time-honored options of "--include='*/' --exclude='*'"
would work fine in place of the hide-filter (if that is more natural to you).