Sometimes i find when only half of images are aligned, it is not because half the images are bad but because photoscan finds two subsets of images that can be aligned, only not with each other. Since it cant align the subsets to each other it just shows one or the other and leaves the other 'not aligned'
to see if this is the case, duplicate the chunk, then reset alignment for aligned images in the duplicate chunk, now select the images in the duplicate chunk that were not aligned previously and right click -> align selected images. You may find that now the other half of the images are aligned in this duplicate chunk.
if you are lucky you may be able to align the two chunks together using the align chunks workflow process, or you may have to take some more photos at the joint between the chunks where the overlap is not sufficient for whatever reason. if you have pro version then you may be able to align using markers.