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Assuming the PDFs have a text layer; why not just search the content as and when you're looking for something using something like Windows Search, MacOS Spotlight, or one of the Lucene based tools on Linux.
The "Drop Search Results (DSR)" plugin can be used to Mark the books most Windows search tools find in a calibre library, from there you could create a Reading List (another plugin), or tag the books.
Another alternative might be to use the Multicolumn search plugin, it claims to have full text search capabilities.
BR
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