It is a little hard to understand you - but is "versioning" what you are trying to make?
So that can "go back in time" to find an old version of a file?
Then --backup-dir is a function you will want to use. Please read the link asdffdsa provided.
Asdffdsa and me actually made a script that does this (timestamped versioning) for someone else:
Unfortunately this is batch-script (for windows), but the rclone commands would be basically the same, and it would not be so hard to translate this to bash-script for Linux. You can just use our script as an example if you know bash.
That script creates dated versioning, so that you can go back to any date where a file was "deleted" or "overwritten" and recover it - because instead of actually deleting it will be moved to a timestamped folder.
Please let me know if I need to explain in simpler english, or if I have misunderstood what you need 