As
MxxCon suggested, create a queue and save it, then put the following command into your schedule:
"<full path to flashfxp.exe>" -go -c2 "<path to your queue file (.fqf)>"
You might want to uncheck the "Exit with non-empty queue"-confirmation in the options, to be able to let FlashFXP fully close when done - even with failed files (which normally is automatically saved and can be found in "Restore Queue" later on).
Hope it can help you out
