The scan software you used to create the PDF file with...do you know which version of the PDF format it creates?
If it is an older PDF format, you might be in luck finding (open source) software to repair or recover your data from. Maybe a copy of Libre Office or Open Office (both open source) is able to read the "mangled" file(s).
Newer PDF formats have much more "trickery" build into them. Even if those new features aren't used in your generated PDF, it is highly likely that repair is much more difficult and possibly costly to recover/repair.
If repair isn't a possibility, would it be too difficult/Time-consuming for you to regenerate these PDF files (perhaps using an older/simpler version of the PDF format while you are at it)?