Hello,
If the deleted directories were empty, you can just recreate them by any usable protocol: SSH, FTP, FTPs, Directadmin manager
If you had content under the directories you need to recover them from backups, and if you have no backups probably restore your VPS from a snapshot created by your server provider.
If you have no backups and no snapshots, then you will need to re-create your site(s).