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If you are running in Algorithmic mode, one option is to write a "Server Finalization Script". This would be a bash script that loops through all the datapoints on the OpenStudio-Server filesystem and uploads them to s3. This script should still run even if there are datapoint failures.
(You might be able to use the "Worker Finalization Script" instead, but it runs once per datapoint and I'm guessing it doesn't run if the datapoint has a failure? I'm not positive.)