As long as you haven't done any manual painting or set up any Uv dependent texture masking these filters are derived purely from your baked maps compare the baked maps from before and after your model change - if there are notable differences then you have your culprit
I feel your pain. Painter is a non-stop puzzles maker . In my experience it's some baked random poly-group id colors or mismatching AO that is included in your masking or gazillion other reasons you may waste a day trying to figure out. It's exactly why I prefer Substance Designer even for 3d objects texturing. At least…