Here's a recipe for creating the problem.  It is not completely
deterministic, but it seems to do it about half the time.  This at least
suggests the failure may be partly skanlite specific, though it may be
in interaction with other systems.

1. Preview a document after enabling "automatic selections", which is
the default.
2. My document typically gets 4-5 red boxes.
3. Highlight the entire area of the document.
4. Press scan.
5. This will scan each red box in sequence, and then the whole page.
6. For the first few, hit cancel in the popup window that allows you to
save the image.
7. Then, in the main window while an image section is being
scanned--i.e., scanner is physically scanning and progress bar is in an
intermediate state (also worked once with it at 0% but scanning in
progress) hit the red button to the right of the progress bar.  This is
not the red cancel button which is immediately below it.
8. Next region scanned results in "device I/O error".
9. skanlite will not work (i.e., device i/o error or, if relaunched,
failure to detect a scanner) until reset by physically disconnecting USB
cable.

I have never got a failure doing step 7 before the 3rd subsection to be
scanned.  I have got a failure doing step 7 on the final scan  of the
whole page.

Step 7 does not always cause a failure.

Oddly, there are no messages in /var/log/kern.log (except when I
reconnect the scanner) or .xsession errors.  Perhaps running udevadm
monitor caused them to be redirected?

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