If the latter, does that prevent exit through a barrier at the destination station?
I'd also be concerned if this happens when break of journey is possible
It shouldn't usually. If the person on train clips it then their device is usually set to the train they are operating. If the person scanning the ticket is at a station where your journey ends then the gate or person who has scanned the ticket is effectively marking it as completed and it won't be accepted by another ticket gate.
Usually they won't scan at intermediary stations, for example when changing trains or having a break of journey, however when scanned by a staff member they can still mark the ticket as being checked at that station. This shouldn't impact on the ticket in the same way someone writing on a CCST ticket wouldn't on a multi train journey. One handy thing is that there is much more data so you can see when and where it was scanned, so if the passenger is off route for example and the ticket has been checked along the way its easy to see where they've "got lost" so to speak.