I noticed the journey progress for SEH is not transferred to TSW3. For other routes it is working properly. I can imine there are some problems in doing this, given the timetable is reworked, but even scenarios completed with gold are not marked as completed. This is nowhere documented as a change and it should have been documented at least. Now it comes as an unpleasant surprise.
I suspect because SEHS has been overhauled and has a new timetable? As you say every other route Journey progress carried over, though I haven’t checked Bakerloo. Wouldn’t be surprised if that reset due to having a different timetable.