Sometimes a file doesn't show up because the filename contains "funny" characters. This usually means characters that aren't 7-bit ASCII. For example, I sometimes convert blog posts to EPUB files for later reading. For some reason, many blog post titles contain an 8-bit character that looks like this: >> . I always have to delete this character from the filename for the file to show up for me to read on my Kobo. The same holds for PDFs as for EPUBs.
What I recommend is that you delete all funny characters from the filenames of all your problem files. You might even try renaming them test01.pdf, test02.pdf, etc. as these names are absolutely safe. Then see if you can read them.
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