Southern run these: http://www.realtimetrains.co.uk/sea...19/04/01/0000-2359?stp=WVS&show=all&order=wtt
They appear to be one half of route SN3.11 / SN 3.12 from the GTR 2018 timetable consultation.
So perhaps they will continue on to Blackfriars once there is platform capacity freed up at Blackfriars. Combined with the existing Thameslink routes this would provide 4tph in both directions around the loop in the peaks.
I think it's a separate BFR-BFR in the opposite direction around the loop of those southern services we have now (i.e. clockwise am, anticlockwise pm) giving the 4tph in both directions around the loop as you suggest. I think those southern services to/from LBG will stay as they are.
I was also on the platform at Ely at that time this morning - I couldn't believe it when they didn't run that train in service! Not only had previous trains been cancelled as you mention, but the 0948 was also already showing as cancelled. So they could have run it as either a "delayed" 0917 immediately, or waited for approx 15 minutes and then run it in the path of the cancelled 0948!