Things vary from operator to operator, e.g. whether frequencies.txt is used. You'll have to see what you can piece together from static GTFS and GTFS-rt.
As far as the case you describe is concerned - depending on how they work, bus dispatch/train control might add a trip by copy/pasting from an existing origin trip, and setting the stop times of the new trip from a start time they provide for the new trip. There is a chance you can look up the origin trip from the new trip's trip_id following the "ADDED_" prefix. With that, you have the reference data for generating the new trip's stop sequence as well as the stop times.