Hopefully that worked out for you. 100km is a huge area! At the end of a typical day of flying, I will be uploading images for about 8 different flights. All put together, they could cover a similar area as what you’re describing. I asked once about having a better folder structure and segregating or naming images by flight. The answer I received was it’s a DJI protocol and DD has no control over that.
My method for uploading multiple flights has been to navigate a DD webpage to the upload dialog, duplicate that tab as many times as needed, and then drag and drop the images from a file explorer window, using the timestamp to tell me where the breaks are (for this to work, I had to customize the “details” layout in my file explorer to show that data). Doing it this way, I have no need to manually adjust the AOI. When a flight spans multiple folders, I drag and drop what I’ve got in the current folder and then use the “Add” feature (that appears after it runs the metadata check) to add in the rest of the images from the next folder. I know what order they were flown, so this works for me. I also do not click the upload button until I’ve prepared the uploads in all the open tabs, then I let them all go and leave the office for the day. On my machine and network, I can have up to 10 uploads going simultaneously. It gets sketchy after that.