Have you already tried just reinstalling the latest version on top of it? It shouldn't make things any worse (and won't affect any settings), and it might just fix it without you losing your settings in the process
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If you *do* want to start from scratch, assuming you don't actually want to backup anything first, you can just remove the koreader folder and then reinstall it.
Document-specific settings are stored alongside the documents in the sidecar directories, so the only thing you'd lose are global settings (and most of it is from settings.reader.lua and the settings folder).