What node is the timer a child of? And is the script attached to a node that is part of the deleted scene?
I suspect your timer or yield was trying to work on script that was part of the swapped scene. I have some projects that assemble the active scene from a landscape (loaded) and several random elements (loaded) + a player character (also loaded)
All these exist in a session node responsible for loading and unloading the parts. The session node persists for the duration of the engine's run and parts are swapped in and out.