I haven’t got time to perform further tests, but I thought of something that you might want to try:
You can use rclone sync with the --backup-dir flag. That way, instead of overwriting files, rclone moves old files away. Maybe you can supply an argument such as a timestamp for that flag.
P.S. Don’t set the destination of sync to the root (Failed to sync: source and parameter to --backup-dir mustn’t overlap)
P.S.2 The docs say When using sync, copy or move any files... but this flag doesn’t seem to work with commands other than sync. Is this expected? @ncw