Problems with a large project

I have attempted a large project of of 983 images and close to 10Gb data to see what happens: Flight ID 1453472561_IANOPENPIPELINE. I was surveying vegetation in a harbour. I flew the mission in four battery charges and there were two flights that did not load correctly at first but eventually flew OK.Would be very useful if I could create this size projects. Segments of the scan were not included in the returned result so I resubmitted the flight in four sections - each within the size parameters. Again the same areas as before were not included in the returned results. I have had a lot of success to date with large projects but I can’t figure how to get this one to work.