That is not fun... This is something either internal to the camera or caused by corruption in the SD card. Map Pilot doesn't do anything other than tell the camera to take a picture.
As long as the mission had plenty of overlap (80% or more) it will likely be fine without those images as long as that section isn't right over a bunch of bare trees or something.
Merging the images in is possible but it is hard to do well. Unless you can match the exact time of day and lighting conditions it will likely do more harm than good.