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You can now configure whether you want to allow files with the same name to be uploaded to the same folder (or at the root level.) This can be configured in S-Drive Configuration under the General Settings Tab. You can read more here under See Upload Settings for more information.
Chatter File Sync
When File Sync is configured to delete files after syncing, this causes files in Chatter to seemingly disappear. Now when Chatter files are synced to S-Drive there will be a message in Chatter that files have been synced to S-Drive and a comment will contain the names of the files. See what this looks like in our File Sync documentationwith Chatter for more information.