You could display all of your adjacent and overlapping sites and just draw a new one that covers the whole area. There is no automated way to merge saved flights. There may be a way to do that in the future.
Breaking large areas up into smaller areas is the right thing to do. If you plan on processing them together in Maps Made Easy we recommend having at least 1 pass of overlap between the adjacent saved missions.
Handing images is always hard. It is really best to get into good data management habits and have backups. Always use the files directly as they come off the SD card and do not use a photo management software since they can destroy image tags permanently. Since the images are on the SD card on the aircraft this isn't really a step that most companies help you manage.