It was just that I switched to "connect to folder" in Calibre and ended up with two sets of metadata (though moved books to a different folder in the mean time), and assumed my search issue was related.
I carried out a search for a book, which Koreader found, but I got a file does not exist error when I tried to open it (though I could open it fine in file explorer). I think it might be a comma in the filename causing an issue?
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