flashfxp doesn't pre-allocate disk space because then it would be impossible to resume incomplete transfers.
flashget keeps info of what was downloaded internally, and it's usable only by flashget, nothing else.
flashfxp, or any other ftp client in the world would see that a local file is x bytes but remote file is y bytes and it'll be able to resume transfer knowing exactly which bytes to get.
disk fragmentation is a pretty insignificant thing. it can be easily addressed by running a defrag once a night or even once a week.
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