"so far I have tried" refers to actions that had no mentionable effect on 
the result, meaning that the issue is probably not with them 
individually... which you confirmed, but well, I tried.

So the first step is to check the intermediate images. Have the remapped 
> images already the black spots? Or have the merged stacks these defects? Or 
> only the blended panorama?
> So this is the first questions to be answered.
>
 
For clarity I will use the word "gap" to refer to what you call "spot." I 
regularly see other spots from remapped images in the preview which are not 
present in the final render.
When I output layers today one of the layers ended up with a gap. Adding 
control points to that layer moved the gap to a different layer, and adding 
control points to that layer moved it back to the first. At this point 
there is an average 0.4 error on the stitcher.

*But the main question is unanswered. Which tool produces the black spots?*
> *For HDR output there are several tools involved:*
> *1. remapping with nona*
> *2. merging stacks with hugin*
> *3. blending the stacks with enblend or verdandi (internal blender)*
>
 
Since there were no error messages or logs that would return an error, I 
believed the problem was with enblend in this particular panorama - it 
broke an image with at least 80% of layers remapped properly. It could be a 
remapping issue, but that would probably show gaps when inspecting images 
in the preview/drag/move tab?
I need to point out that here two of the image stacks overlap just barely, 
probably 1/5th right on an area with low contrast (hazy area on the left 
from the sun). While they stitch badly there are no gaps there.

... 

> * blending with internal blender and soft seam (select under internal 
> blender options).
>

In this case both - enblend and builtin had the same problem, though I 
don't think I tried with soft seam (will do). Blending with nearest-feature 
did not have noticeable effect. On some of previous images builtin returned 
a panorama without gaps (spots), but all seams were strikingly visible...

Other notes for anyone experiencing similar issues:
*Photometric optimization results in high values *- consistently I find 
that when photometric optimizer calculates an EV range around 20 stops or 
more, it means that the exr panorama will have a spot [gap]. I suspect this 
is because the colour under it is much darker than anything in the actual 
scene.
*Stitch panorama from EXR stacks* - I was unable to finish through this 
method due to not knowing which output projections to set and how to read 
them in again properly. Projecting each stack to to equirectangular and 
raeding back from it seemed like a good idea but did not align properly 
(yet).


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