You could set an OnTimer script to do that (Save a copy as..., then select compacted copy) and run it from a client that stays open. Beware the solution should not have a Kill-step for OnTimerScripts anywhere in other scripts.
You must change the folder name to prevent errors when creating a copy of the same name.
Unfortunately, server-side script will not allow this, but if you are using FMServer, it is easy to schedule a backup there.
There is a script step to save a copy, which lets you set it to a compacted copy.
I use this for client-called Backup scripts all the time (not automatically triggered), adding a date-stamp to the copy saved via a calculated file name from a $variable.