What you can do right now is mark all the files in the queue and press CTRL+F. Later on, you can mark them again, and press CTRL+R - or if you have no running transfers left, simply press CTRL+Z.
The other possibility is to quit FlashFXP with a non-empty queue. So you can use the queue later. But this is no option for you if you filled up the queue with other things already that you wish to continue on right away.
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