There didn't seem to be a way of handling it, so on a project that needed to upload files to S3 they hacked the module to add a timestamp to the filename. This has been reworked so now instead there's a drupal_alter() hook prior to files being processed.

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DamienMcKenna created an issue. See original summary.

DamienMcKenna’s picture

Status: Active » Needs review
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This is the patch we're using.