Using mongodump/restore as the mode. All collections were marked as downloaded correctly. About 60% were marked as uploaded. The job was marked as completed and did not continue uploading.
I manually flipped the "completed" flag to false in migrationjobs/list.json and resumed the job. In the log it shows a bunch of "added to upload queue" for the collections that weren't uploaded yet, but they do not get uploaded, instead the job flips the completed = true again.