I'm trying to remember where the rapture showed up... I think, for me anyway, it showed up in the middle of the river, east of Ivrstead. It was only a few glowy wisps, kind of like a Spriggan when it goes invisible(ish).
Was almost hard to find if it weren't for the marker.
If you were at the spot, and had the staff of magus, try using the staff in the direction of the arrow.
Once I did that, three little glowy orbs popped out, like in the battle at winterhold.