Here's how I would do it.
Connect to each site one at a time and queue the folders that you want to upload, when your finished you'll end up with one queue file that contains all of the information you need to perform the transfers on each of the servers.
Once you have the queue file you can run FlashFXP via Windows Schedule with a command line, check the command line section of the help file. something like FlashFXP.exe <queue file>
Future versions of FlashFXP will provide a direct interface to Windows Scheduler to make this even easier to configure.
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