Charles supports a few command line options out of the box, documented here.
Unfortunately they seem to operate only as parameters for new Charles sessions, so you won't be able to run commands on a running instance of Charles.
Start a specific Charles session
A Charles session contains all of your recorded information. It is represented by the Session window; by default a new session is automatically created when you start Charles.
Sessions can be saved from File → Save Session (⌘+S).
Once saved, if you want you can start Charles from the saved session by running: