Dear Novalesk,
Generally, you can just create the master Excel file in a site library in SharePoint Online>open it in Excel Online>Hyperlink>copy the URLs of the files in it to create the hyperlinks.
Then share the PDF files, the documents and the workbooks with the auditor. When the auditor open the downloaded master file, he can click on the hyperlinks to access the files.
If something is misunderstood, welcome to give some examples about your requirements for our further clarification.
Best Regards,
Cliff