For Alpha 6 I left the files and Transmission in the prior state (Alpha
5) and fired up Transmission. Both torrents in Transmission were
highlighted in red and said "Requested download is not authorized for
use with this tracker - idle".

That also jogged my memory. For Alpha 3 -> Alpha 4 experiment I now
remember having three torrents, the two new Alpha 4 torrents and one in
red (the Alpha 3 with both the old torrent and the old Alpha 3 jaunty-
desktop-amd64.iso file. I now remember deleting that "dead" torrent but
leaving the old iso file, which after download was complete didn't pass
the checksum.

So while I was warned about the torrent I wasn't informed I needed to
manually rename or delete the target file. This warning or rename /
delete after prompting the user needs to be taken care of when adding
the torrent via a link (for example clicking a link on
http://cdimage.ubuntu.com/releases/jaunty/alpha-6/) and also when
removing an "idle" torrent from the Transmission UI.

Hope this helps clarify. Thanks for your interest in improving
Transmission!

-- 
does not handle updated file images with changed md5sums
https://bugs.launchpad.net/bugs/318249
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