Prevent rsync from deleting destination files that match a given pattern
You can exclude files/directories with --exclude. This will prevent the somedir directory from being synced/deleted:
rsync -avrc --delete --exclude somedir source destination
As mentioned in a similar question, this can be accomplished by using the --filter option with protect rule:
$ rsync ... --filter 'protect /remote-directory-to-keep/' ...
Unlike the currently accepted answer, using --filter is useful, for instance, if you also wish to use --exclude with --delete-excluded.