I got all the way to the end, whilst defeating the main boss and getting data spikes, I died from misadventure somehow, whilst I was about to use the green teleport / boost thing. Then as a result the data spike dropped into it and there was no way to get it out. I had to quit the mission and will have to do it again. :(
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How long did you wait? After a minute or so the harpy should respawn so you can get a new one