User can control the versioning of the files before sending them to Amazon i.e. you can add or remove the version number added to the file.
On the About Page, Turn off the file name versioning toggle to remove the version number appended to the file.
Note: If this toggle is off and you are trying to upload the same multiple times, it will create versions of the File in Amazon and will not upload a new file each time of migration.
PS: View Drag, Drop & Upload Files to Amazon S3, a Salesforce AppExchange app for moving files from Salesforce to Amazon S3: https://appexchange.salesforce.com/appxListingDetail?listingId=a0N3000000B5ZPqEAN
