Auto FTP Manager can move your files to a different folder after they are transferred.
Here are the steps:
1. If you have already created an
automated transfer profiler then select the profile and go to
File >> Edit Profile.
2. On 'Specify Automated Transfer Settings' dialog, select the action rule "After transfer move files from [Source] to [Folder You Select]"
3. Select your destination folder using the "Location..." button
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As each file is successfully transferred, it will be moved from the source folder to the folder you have selected. Your files will be removed from the source folder.