I move the panorama so that the translated shot is centred in the preview
window. E.g. by 0,90,0 (pitch up 90 degrees for a nadir).
I then stitch it (usually rectilinear) with up to 90x90 degrees.
I then create new panorama, stitching the normal equirectangular
output(0,0,0) with the 90x90 patch
Yes I know it takes more effort and is a workaround not a fix, but it is
effective.
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