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Email mapping@dronesmadeeasy.com directly instead of using the web form if you aren't getting the responses. If there are failed uploads the DJI workflow will as you if you are sure you would like to continue without them. A few missing files is OK, but not anything more than a couple percent.
Yes, if you are getting upload failures it is best to cancel the rest of the upload and figure out what is going on. It can help to try another browser, computer or internet connection. Make sure the computer doesn't hibernate when uploading since that will interfere with things.
You should try doing some smaller works first to learn how to use the system before jumping right in to doing 3500 images.