If everything else fails and you end up with a new system or a newly installed fresh HD in the old one, you can keep the old HD externally and later attach it to the freshly installed system, trying to extract those PDFs. I would do so only if it is verfified fact that the HD had a technical problem and no software-induced one: malware in other words, else you would just infest your new system with the old problem. If software or "unknown cause" is the problem, never attach the old HD to a new system again.
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If you feel nuts, consult an expert.
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