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seems similar case https://repost.aws/questions/QUfuhk5RyCTci-9UF0LNXxYg/continue-s3-file-upload-from-where-it-crashed
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verify the parameters multipart_threshold, multipart_chunksize try to bump values and see. https://docs.aws.amazon.com/cli/latest/topic/s3-config.html use_accelerate_endpoint would help too.
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I added the variables suggested in the mentioned post:
max_attempts = 20 retry_mode = standard
With this I was able to upload it manually once. We will see if the problem will actually be resolved as the script runs over the days.
Thanks!