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Saving to disk will not affect your calibre library. It creates copies of files. In fact calibre never makes changes to the copies in its library, to ensure they can never be corrupted.
Saving to disk however updates the metadata in the copies it creates. It is probably that that is causing the corrupted PDF files. You can fo to Preferences->Plugins and disable the PDF metadata writer plugin, that will make this problem go away.
The only thing I can think of that could cause this is if you used some other program like windows explorer to manipulate the files in calibre's library, or you accidentally used the library folder as a save to location
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