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There is no difference between pdf and epub for the search.
Are the epubs in the same metadata.calibre file? I still susepect you have two of them, and the second is not matched by SEARCH_LIBRARY_PATH2 anymore.
Open /mnt/us/metadata.calibre with a text editor and search for any epub file. Then open Koreader and search for exactly this file. Long tap on the search result and check the info on bottom, the path, plus either the file size or "file not found".
If file not found, compare this path with one of the PDFs that is working.
And if you have a second metadata.calibre anywhere set SEARCH_LIBRARY_PATH2 to the directory where you found it.
Also delete the "temp" folder within Koreader (or at least the metadata.koreader file in it) since this one is caching the results, and if something is wrong you still might get the wrong results.
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