Syncing a source directory that contains the destination directory is never a good thing. I can't tell you exactly why the destination directory appears to be disappearing, but it probably has something to do with trying to replicate the directory recursively.
To avoid this, use
rsync with its
--one-file-system option. This stops
rsync from entering other filesystems on the source side other than the filesystem that the top-level source directory is located on.
This would however not work if the destination directory is mounted as a "bind mount" inside the source directory. In that case, you may instead explicitly exclude the destination directory with
--exclude=/destination_directory (I can't unfortunately tell you what path to use with
--exclude here as you are not showing the actual paths in your command in the question).