It isn't automatic, but just open two or three session windows and start downloading with all of them. You can even load the queue from the first into the others so you don't have to re-queue stuff. Flash will figure out that it can't open for writing a file that is being downloaded by another copy and just move onto the next file. It will mark the download in the queue as failed, but just ignore that at the end...
Tip: sort the list of files in the queue in the first copy, and then reverse sort it in the second instance so two copies won't be trying to download the same file repeatedly. In the event you run into a large directory in the middle also set the remote directory listing to sort the reverse way of the first copy so when the directory is expanded into the queue it will be entered in the reverse order as well.
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