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So I had a quick look through the code just to see if I could figure it out, and I think I've narrowed it down more -- the error only occurs if there's a book on the device which isn't in the Calibre library.
I started looking through the lines mentioned in the traceback, and line 239 was weird, because it's the call to update_device_database for the main memory. The only book left on the main memory in my reader is the user manual; all my other books are on the MicroSD card. And sure enough, when I deleted that book and uploaded a copy of the manual through Calibre instead, the error went away (and the covers for my other books got updated as I was hoping).
If I copy the original manual back into place without using Calibre, it brings up the error again on the next connection. And if I copy the original manual back onto the MicroSD card instead of main memory, the error comes back and refers to line 241, which is the update_device_database call for the MicroSD card. So I think it's actually choking on that non-Calibre book when it sees it. The same behaviour occurs with other EPUB files that aren't in Calibre, so it's not just the manual file.
Hopefully that helps to narrow it down. In any case, I have a perfectly good workaround for my usage -- I'll just leave the Calibre'd version of the user manual on the T1 instead of the original.
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