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Going through the files, I noticed that now there was no files named KUAL (aside from KUAL.cfg). There definitely was something before logging out and in, so it must have purged the KUAL booklet during that process.
Having noticed that, I have re-installed KUAL using mrpi, which seems to have worked - all the entries that used to be in KUAL still are, and koreader launches again.
After a bit more poking around, all my settings and everything looks to be as they were. If I discover anything wrong, I'll post an update here.
Now that it's working again, what would be the best way to find logs so that the underlying problem can be identified?
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