I have a 360 / 180 pano where I forgot to shoot a nadir shot. When I assemble it in APG, it gives me empty pixels all along the bottom.
That´s what it´s supposed to do.
If I use the pitch tool at 90 degrees, this empty area comes up as a much smaller roundish patch in the middle of the pano.
Don´t do that. Instead use the following workflow:
Drag your equirectangular rendering onto the KRPano-droplet: "convert sphere to cube". This will give you six cubefaces.
Take the down-face - this one shows the "Nadir-hole". In Photoshop you can easily retouch it using the stamp-tool.
After that drag all six cube-faces to the droplet "convert cube to sphere". This one will give you back an equirectangular image with a
You can find the KRPano-Tools in your PTP-folder if you have a PTP license.
You also can use PTP for making cube-faces - but i always use the KRPano droplets for doing it.