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Yes with new credentials any object that has already been transferred won't be retransferred. However if one object is particularly large and will not complete within 36 hours even though the s3 sync commmand will use multipart upload you cannot resume from failed uploads in this scenario - see docs. You could run a multi part upload on large file which you can resume using the lower level cli commands - see here.
You might also want to consider using AWS Datasync if this is a process which you will be running regularly.
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