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It's definitely not the uuid, as I've completely wiped out FBReader in case it was some sort of cache. (cleared its cache and data, and deleted any related directory for it)
When I looked at the books that don't show as being part of the series, or show up as unknown author (another example) I think I see the difference in the structure of the epub. On the ones that show up correctly, all the html files are in the root of the epub, but in the ones that don't they're in a sub folder.
So I think this may be an issue with FBreader specifically, but I'm still curious to find out what's happening.
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