Any polygons touching the pad you’re editing will get added to the pad body when you exist editing mode
Press cmd+e to exit pad editing mode
Layers
make sure any copper pads also have the proper silkscreen mask layer selected. Footprints are usually designed on the front copper layer so also select the front mask layer. Otherwise your pads will be purged correctly but will get covered in silkscreen. I did this on accident and you can still scratch the silkscreen off but it’s annoying. Also it screws up your stencils.