It reminded me of a fic I read where Sherlock revealed himself to John through an app, only it was Sherlock spying on him and responding live.

I could see Sherlock breaking into Lestrades office and replacing the dvd with a copy that has a program in it to open up the web cam, or simply having a web cam in the flat and responding to him from Baker Street in real time. There is a momentary change in scene from the wall paper to sitting in the chair. That could be when the change is made. That would explain how when John said "Don't be dead" Sherlock could say "Okay". And how when John hit pause, Sherlock paused for a moment and then winked anyway.
Or it could have been Sherlock at the door.