Yes, FlashFXP can do scheduled transferes. You can use FlashFXP's internal Schedule feature (under Tools > Schedule), which does require FlashFXP to be running.
Or you can use Window's Task Scheduler (normally under Start > Programs > Accessories > System Tools) combined with FlashFXP's command line options to automatically load and transfer a saved queue.
You can adjust how FlashFXP should handle existing files for all sites (under Options > File Exist Rules...) or for a specific site (under Site Manager > Options > File Exists Options). These rules look at both filename and filesize.
Hope this helps.
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