Either we know what you want or you can read our minds
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We're working on both of these features for the next FlashFXP release. The backups won't be automatic but it will just be a few clicks.
You can create your own automated backups by backing up all of the *.dat files and the flashfxp.ini. Depending on your installation options the *.dat files may not be stored in your FlashFXP folder but rather the Application Data folder.