the only solution is to run the batch using Scheduler.
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Yes, upload the files using Scheduler and add an Event that runs after a successful file upload to run an external script to move the file to your archive folder. You have access to the $LocalFileName and $LocalPath to pass to this external script. Doing it this way, only those files successfully uploaded are moved to the archive. If there is some error with the upload, then the same file will be serviced next cycle. Note: your external script should probably handle filename collisions in your archive folder or else you will upload the same file over and over again. (Speaking from experience.)