The way this PCB representation is made in KiCad is very problematic. It doesn’t have footprints at all which would have copper pads (it has only NPTH footprints, mounting holes). Everything is done with vias and graphic polygons. KiCad understands zone areas to be connected when they touch pads. Because you don’t have copper pads at all, zones aren’t really connected. See How to create a power plane (using zones) for further information. Actually, I don’t understand how your zones have been filled in the first place. Maybe I have to dig deeper.
BTW, your 7zip archive includes kicad_prl file. That’s the “project local” settings file which saves the state of the GUI and shouldn’t be shared. It only creates confusion because now you had hidden many objects and when someone opens the project there are for example no visible footprints.