Hi, you will have to use the --backup-dir option with the sync command, providing the directory name with some environment variable that references the date and / or time, depending on your need.
I use rclone sync as a backup. The following is a sample script I use:
DATE=`date +%Y_%m_%d_%H_%M_%S`
NAME="Vault" #This is the hard drive name I'm backing up. I have different scripts for different hard drives.
LOG_NAME=$NAME\_$DATE.log
rclone sync /Volumes/Vault MY_DRIVE_REMOTE:/Backups/iMac-Late2012/Backup/Vault --backup-dir=MY_DRIVE_REMOTE:/Backups/iMac-Late2012/SafetyNet/Vault/$DATE --exclude ".DS_Store" --exclude ".DocumentRevisions-V100/**" --exclude ".TemporaryItems/**" --exclude ".Trashes/**" --exclude ".fseventsd/**" --log-level="DEBUG" --log-file=/Users/andyibanez/rclone_logs/$LOG_NAME --checkers 1 --transfers 8
Each hard backup session will create a new directory in my SafetyNet directory where it will place deleted and modified files since the last sync.