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 found out another way things get out of wack (idk if they fixed it) is if you move any part of a model and try to reimport it say posed or any part repositioned. Will "destroy" smart masks which then makes them not so smart, the same with many other "smart" things, "funnily" ironic to me. So solution for me was to not…