My first thought about images rendered black was that somehow you are
(well, Hugin is) using a wrong value for the EV. Normally you can
tweak the EV value (in the preview window, for instance) to alter the
brightness of the image. If the EV is set to a very low value, the
image will be rendered completely white, and if set to a very high
value, it will be rendered completely black. Is this the case maybe?

Regarding the final image. I don't know if the zoomed in images cover
the entire low res panorama, but if it does, the simplest solution is
to remove this image from rendering by clicking the image number once
in the preview window. If all positions were already correct, this
will leave you with a high resolution panorama with all the data
coming from the zoomed in images.

I hope this helps a bit.

Best,
Bart
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