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When searching within a library it finds PDFs that are within a title, but it does not find PDFs that are at the top level of the Zotero tree structure.
Thank you for your interest in Qnotero and for taking the time to report this.
I filed an issue. I suspect this won't be too difficult to fix.
There's much bigger issues in the world, I know. But I first have to take care of the world I know.