I've had trouble before using Hugin to stitch panos which have a featureless Zenith shot with no distiguishable points, such as a clear blue or dull overcast sky.
But I invented a little Cheat to get a round it using Photoshop.
Remove the problem zenith shot from the project and process the stitch without it.
Load the stitched pano into PS, be sure to alter the Canvas Size, anchored at the bottom to make the image a 1:2 aspect.
Load the problem zenith shot into PS.
Use the Filter - Distort - Polar Coordinates... Set it to "Polar to Rectangular", that will unwrap the centre of the image to the top, as in a 360x180 Lat-Long image.
Copy and Paste the zenith into the stitched pano.
Use Tansform - Scale with Snap on to make the zenith layer fill the blank top part of the pano, stretching and snapping it into the top corners, bring the bottom edge down to make sufficient overlap with the stitched pano image.
Create a Layer Mask for the zenith layer. On the layer mask drag out a vertical gradient covering the overlap of the images, hold Shift to make sure it is perfectly vertical and matches at the left and right edges.
You may adjust the blend on the layer mask further with a soft brush, but don't touch the edges or they won't match up, though you can get around that using the Offeset filter (moving only horizontally) afterwards, then retouching the edge when it's not at the edge.
In fact the horizontal offset can be used to effectivly rotate the zenith to mach the orientation of the pano.
Adjust the Levels, colour balance etc as required to match the zenith with the rest of the image.