I am not sure what you are looking at that you see duplicate file names, but each data set is its own entity. Lets just work with one data set for now. It contains images 1 through 637. There are no duplicates. If I upload all those images, it leaves off the whole top portion of the map.
To answer Saiins question. It was flown at 250 feet at 4.5mph, shutter speed is 1/200 at f/5.6. The Autel has a mechanical rolling shutter which I do not believe can be turned off. However, I also flew three data sets with a Phantom 4 Pro V2 which has a mechanical shutter at the same altitude. Camera settings were the same. I also collected a data set with the P4Pv2 at 300 and 350 feet and same camera settings. Results were the same on the map output. The top half does not get stitched. It is as if the server just overlooks the images from that area. Interestingly enough, If I just upload the missing section, the server stitches them. But why does it not include them when I upload the 637 image job?
I never had this problem before. Normally, I just upload the images and everything gets stitched.