Am I going to hate myself for applying new membrane over this?

New leak noticed inside after freezing rain, right about where the pitches meet. This membrane is 2 years old, applied when we bought the house as part of seller assist.

Looks like it was maybe applied over some serious issues? There are some squishy places. So it seems like my options are rip the whole thing off, replace decking, tar paper, EDPM maybe, basically reroof the shit. Or slap some new elastimeric coating on it and deal with the water damage from underneath.

I have about 1.5 years home remodelling experience and feel confident in my personal skill but I'm unsure of the scope of this one. Never did many roofs.

Thanks y'all! I'm gonna be on the phone with the permit office on Monday just to get that out there.