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I use windows junctions to create a link to the "finished torrents" folder.
Sometimes when I delete an unfinished torrent (and delete the data), it deletes the "finished torrents" folder. I can recreate the link, but then qbittorrent insists on rechecking all of the files.
More details:
r:\qbittorrent contains links (junctions): qTorrents, qTorrentsData, qTorrentsInc, qTorrentIncData, and torrents. All are windows junctions to other directories.
Sometimes, if I delete an active incomplete torrent (which is in qTorrentInc and qTorrentDone), it correctly deletes the torrent I specified, but then (incorrectly) deletes the link to qTorrentsData. I get immediate io errors.
I haven't tried to reproduce it, but it's happened at least three times.

I can now reproduce it.
It only happens when the incomplete torrent has no data, and hasn't yet created a partial data file in qTorrentsIncData. If I delete such a torrent, it deletes the qTorrentsData folder (which is a junction to the actual folder.)