I have this KiCad project that has multiple PCBs, and i cant get KiCad 3D renders to have holes in all PCBs where there is a circle in edge.cuts, only in one of the five PCBs the holes are present. Have a look:
KiCad only really supports one PCB per project, so either split your project into five, or if you intent to manufacture these together, connect these PCBs manually using bridges and mouse bites or whatever, depending on how you intent to break them apart later. Similar to this: