When the Rep Model is updated in 3DCS, only the Parts involved in the Rep will only get updated to show up in the 3DCS Tree while the rest will be hidden.
Adding any 3DCS data to the Rep will still be stored in the main Master Model so when the user switched the model from Rep to Master they will still see the data in it.
Rep Model saved with 3DCS:-
Open the Master Model of the same Rep and update Model to see all the Parts from the Master Model along with the data added to the simplified Rep:
3DCS data can also be added to the Master Rep and saved.
The user at any point switch between the Master model and Rep and add 3DCS Data but only the information of the selected Rep will be visible in the Tree.