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It looks like you can get around the issue I mentioned before by letting the control/browser connection time out before trying to download anything. But I couldn't find a clean way of doing that in FileZilla (even setting all the concurrency options to 1) without simply waiting X amount of time for the old connection to die first.
Pretty sure I gave up in the end because the delay between the timeout (when browsing) and trying to download again became a major pain.
rare_j's idea of making sure the queue isn't processed until I've finished browsing everything is likely the best route. Didn't occur to me at the time, but yeah, it's not behaviour that people using FZ are likely to be used to!
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